--------------------------------------------------------------------------- CHARMM22.0.b Release April 22, 1991 CHARMM22.0.b1 Release September 30, 1991 CHARMM22 Release January 1, 1992 c22g1 Release February 15, 1992 c22g2 Release July 7, 1992 CHARMM23.0 c23a1 Developmental August 15, 1992 c23a2 Developmental October 25, 1992 c23f Developmental March 1, 1993 c23f1 Developmental March 15, 1993 c23f2 Developmental August 15, 1993 c23f3 Release February 1, 1994 c23f4 Release August 15, 1994 c23f5 Release March 15, 1995 CHARMM 24.0 c24a1 Developmental February 15, 1994 c24x1 Evaluation February 15, 1994 c24a2 Developmental August 15, 1994 c24a3 Developmental March 15, 1995 c24b1 Release August 15, 1995 c24b2 Release February 15, 1996 c24g1 Release August 15, 1996 c24g2 Release February 15, 1997 CHARMM 25.0 c25a0 Developmental August 15, 1995 c25a1 Developmental February 15, 1996 c25a2 Developmental August 15, 1996 c25a3 Developmental February 15, 1997 c25b1 Release August 15, 1997 c25b2 Release February 15, 1998 --------------------------------------------------------------------------- [0] About CHARMM25 Development As an on-going project, CHARMM development will be carried out with CHARMM version 25 series. We set up the base revision c25a0 out of c24b1. The following describes new features and enhancements incorporated during the c25 development period, c25a0 to c25b1. =========================================================================== [1] c25a1 Change Log The base revision from CHARMM c25a0 (August 15, 1995, identical to c24b1) to c25a1 (February 15, 1996) 1.1 Merck Molecular Force Field (MMFF) - Thomas A. Halgren, Ryszard Czerminski, Jay L. Banks, Bernard R. Brooks, and Youngdo Won Merck Molecular Force Field (MMFF) developed by Tom Halgren at Merck has been implemented in CHARMM. Ryszard introduced MMFF into c23f2, which made the c24x1 (February 15, 1994) version for evaluation. As CHARMM was evolved through the c24 development project, Jay incorporated MMFF into c24b1 in a less intrusive manner. Bernie and other developers reviewed c24b1/MMFF and suggested some corrections. Youngdo took the Jay's code and Bernie's suggestions and made the checkin code of MMFF. MMFF is documented in doc/mmff.doc. Files Added: source/mmff/*.src /fcm/auxpar.fcm /ffield.fcm /io.fcm /mmff.fcm /vangle_mm.fcm build/UNX/mmff.mk Files Modified: source/charmm/charmm_main.src /iniall.src /miscom.src /energy/eintern.src /energy.src /eutil.src /intere.src /printe.src /gener/genpsf.src /modpsf.src /update.src /image/eimage.src /io/mainio.src /parmio.src /psfres.src /rtfio.src /minmiz/conjug.src /misc/hbuild.src /nbonds/enbond.src /heurist.src /nbutil.src /pert/block.src /epert.src /pert.src /fcm/consta.fcm /deflts.fcm /dimens.fcm /energy.fcm /exfunc.fcm /fast.fcm /inbnd.fcm /param.fcm /psf.fcm /rtf.fcm /vphi.fcm ------------------------------------------------------------------------------ 1.2 NIH Enhancements - Bernard R. Brooks, Richard M. Venable, and others at NIH 1.2.1 Ewald code The EWALD electrostatic option has been overhauled yet again. Memory needs have been reduced, and multiple parallel options are now supported. Pressure code has been fixed as well. Files modified: source/charmm/iniall.src /energy/energy.src /fcm/dimens.fcm /ewald.fcm /nbonds/enbond.src /ewald.src /ewaldf.src /ewaldf2.src 1.2.2 New substitution variables Box size and box angles are now available as substitution parameters when READCV is called. The variables are: @XTLA, @XTLB, @XTLC, @XTLALPHA, @XTLBETA, @XTLGAMMA, Files modified: source/dynamc/dynio.src 1.2.3 Nonbond and H-bond list update The NBONDS and HBONDS commands will now always regenerate a list regardless of IHBFRQ and INBFRQ values. These changes were made so that some old scripts can still be used without modification. It also makes more sense. New users often wonder why the NBONDS and HBONDS commands sometimes don't do anything. These commands do not change INBFRQ and IHBFRQ unless explicitly specified. The UPDATE command is not changed. Files modified: source/charmm/charmm_main.src 1.2.4 RESD Restrained distance code (RESD) now has a user specified exponent (no longer only harmonic terms). Files modified: source/energy/energy.src /fcm/resdist.fcm /misc/resdist.src 1.2.5 Graphics More graphics enhancements. The no-erase option is fully supported. Files modified: source/graphics/drawit.src /graphx.src /iris_graphics.c /psdraw.src 1.2.6 COOR SEARch The COOR SEARch command has been significantly enhanced. Files modified: source/manip/corman.src /corman3.src 1.2.7 IOSTAT for the OPEN command The OPEN command now returns a substitution variable indicating success or failure. The new keyword is ?IOSTAT. For example, the sequence: OPEN READ CARD UNIT 21 ... IF ?IOSTAT .LT. 0 THEN GOTO NOFILE can be used to prevent CHARMM from dying when files may not be present. This is especially useful when multiple CHARMM jobs communicate with each other. Files modified: source/util/title.src 1.2.8 Mass weighted second derivative write out A MASS keyword has been added to the WRITE SECO CARD command in VIBRAN. This command will cause the actual matrix used in the eigensolver to be printed. Files modified: source/vibran/vibran.src 1.2.9 Particle Mesh Ewald Code The Particle Mesh Ewald (PME) method has been implemented. This code is based on code sent by Tom Darden at NIEHS/NIH. It has been modified so as to conform with CHARMM coding standards. This version is much faster than the std. Ewald code and accuracy does not appear to be a problem when reasonable options are used. This code uses the new "smooth" algorithm. See ewald.doc for more details. Files Added: source/nbonds/pme.src /fcm/pme.fcm Files modified: source/charmm/iniall.src /nbonds/ewaldf.src /nbutil.src ------------------------------------------------------------------------------ 1.3 Contributions from the University of Montreal 1.3.1 A few small changes to MMFP and NMR - Benoit Roux A few small changes to some MMFP subroutine have been made. The main thing is a second atom select for the SSBP command that allows the present of atoms outside the boundary radius. This could be useful when the boundary is used only for an active site. The relaxation time due to the chemical shift anisotropy addition has been added to NMR. See the individual difference files for details. Files Modified: source/misc/mmfp.src /ssbp.src /nmr.src /fcm/mmfp.fcm /nmr.fcm New/Modified Documentation: doc/mmfp.doc /nmr.doc 1.3.2 Poisson-Boltzmann Equation Solver - Benoit Roux and Dmitrii Beglov and Mafalda Nina A Poisson-Boltzmann Equation solver has been incorporated to CHARMM. The facility is called simply by PBEQ from the main input stream. The implementation is still at an early stage of development and only certain features are supported. The PB Eq. is solved on a cubic grid for a cubic box. Other box shape will be implemented in the future. The syntax is straightforward. STREAM files, COORdinate manipulation commands, SCALAR commands and MISCelaneous commands are all supported from within the module. This allows the modifications of charges, atomic coordinates (translations and rotations) and the easy evaluation of the electrostatic contribution to the solvation free energy. In the near future we plan to extend considerably the flexibility of the PBEQ module by allowing non-cubical boxes, the presence of membranes, etc... We also want to implement focusing to a finer grid. The present version is mostly to get us started on all this. Calculation of the charging free energy of all amino acids in explicit solvent is being used to derive a set of atomic radius yielding accurate PB energies. Those should be ready for use around June 1996. Files Added: source/misc/pbeq.src /fcm/pbeq.fcm Files Modified: source/charmm/charmm_main.src build/UNX/misc.mk New/Modified Documentation: doc/pbeq.doc New/Modified Testcase: test/c25test/pbeqtest.inp 1.3.3 WHAM: the weighted histogram analysis method - Benoit Roux A few changes to PERT have been made to make the results of windowing perturbations more consistent with thermodynamic integration. One problem was that the perturbation contributions were not calculated from the correct reference Hamiltonian. Now TP and TI agree very well. In addition, the weighted histogram analysis method (WHAM) as a post processing subroutine for better convergence on the free energy calculations. In the near future we could included also umbrella sampling WHAM analysis routines for multi-dimensional PMF calculations. Files Added: source/pert/wham.src Files Modified: source/charmm/charmm_main.src /pert/pert.src /epert.src /fcm/pert.fcm build/UNX/pert.mk New/Modified Documentation: doc/pert.doc New/Modified Testcase: test/c25test/whamtest.inp 1.3.4 A few small changes to some of the manip subroutines - Benoit Roux A few small changes to some manip subroutine have been made to make our life easier. The main thing is incorporating the ORIEN option into COOR DYNA so that every frames is oriented with respect to the comp set for coordinates averaging from trajectories. Also, the total number of npairs found is the coor dist command is returned in the SETMSC variables (?npair) to allow some control flow over that number (it is used to construct bilayers for instance). Finally, some small changes to remove a bug in shake with regards to PERT (division by zero for TIP3). See the individual difference files for details. Files Modified: source/manip/corman.src /corman3.src /dynanal.src /shake.src New/Modified Documentation: doc/corman.doc ------------------------------------------------------------------------------ 1.4 Contribution form the Scripps Research Institute 1.4.1 COOR DMAT - Charles L. Brooks, III The dist keyword has been removed from the covariance command and a new analysis command has been added under the coor subsyntax. This command is accessed with the command COOR DMAT and provides some general tools for the calculation, manipulation and storage/extraction of distance matrix based properties. This routine has some overlap with the new distance command introduced by Bernie Brooks but also provides significant complementarity in extending the range of properties computed. Files Modified: source/manip/corman.src /corman2.src doc/corman.doc 1.4.2 Port to DEC Alpha parallel platforms - W .S. Young and C. L. Brooks, III A port to the new DEC Alpha parallel platforms using PVM was done by W.S. Young and the Pittsburgh Supercomputing Center in collaboration with DEC. A new machine type has been introduced. USAGE: install.com alphamp size P The addition of the P key queries for where the PVM libraries and deamon is and then allows all subsequent builds to proceed after making a link to the appropriate PVM files. Key for the machine is ALPHAMP and PVMC is used in pref.dat. In machdep/parset.src, catchout call is removed similar to CSPP and SGIMP. In machdep/parallel.src, PVMDATAINPLACE calls are removed. File Added: build/UNX/Makefile_alphamp Files Modified: install.com source/machdep/parset.src /parallel.src ------------------------------------------------------------------------------ 1.5 Contributions from Karolinska institutet - Lennart Nilsson 1.5.1 PBOUND Periodic boxes with unequal length edges are supported. Files modified: doc/image.doc source/image/pbound.src /nbonds/enbfast.src /nbondg.src /fcm/pbound.fcm 1.5.2 SOLANA Enhancement SOLANA is modified to allow the kirkg routine to calculate not only the dipole distribution, but also the dotproduct between the water dipole and the site-water oxygen vector . Also fixed this part of the code to work with multiple sites. Files modified: source/correl/solana.src ------------------------------------------------------------------------------ 1.6 DIMB Enhancements - Herman van Vlijmen The heap allocation of array DDVWRK is taken out. It took up substantial amounts of memory, and was not really necessary. The functions of DDVWRK are taken over by (the already existing) DDSCR vector in most places. Also, heap allocation of PDDSCR (in vibran.src) was taken out, since the DDSCR space can be used for that. The number of modes saved in unit IUNMOD was reported incorrectly in the output file. This has been corrected. Some unnecessary output was trimmed. Files Modified: source/dimb/dimbsub.src /dimbutil.src /nmdimb.src source/vibran/vibran.src ------------------------------------------------------------------------------ 1.7 Enhancements of the Multiple Time-Scale Method - Masakatsu Watanabe New Selection for RESPA MTS method, Short-long range force selection, has been added. Also some MTS defined variable were moved to HEAP. Files modified: source/dynamc/dcntrl.src /dynamcv.src /dynamvv.src /mts.src /fcm/tbmts.fcm /energy/energy.src /nbonds/nbondg.src /nbonds.src /enbfast.src /image/nbondm.src /eimage.src /upimag.src ------------------------------------------------------------------------------ 1.8 Topology/Parameter File Updates - Alex D. MacKerell Files Added: toppar/top_all22_prot_lipid.inp /par_all22_prot_lipid.inp /top_all22_sugar.inp /par_all22_sugar.inp Files Modified: toppar/top_all22_model.inp /top_all22_lipid.inp /par_all22_lipid.inp /top_all22_na.inp /par_all22_na.inp /top_all22_prot.inp /par_all22_prot.inp /top_all22_prot_na.inp /par_all22_prot_na.inp /toppar_all.history doc/parmfile.doc rtop.doc ------------------------------------------------------------------------------ 1.9 Bugfixes (1) Selection of dynamics integrator and Langevin options - Bernard R. Brooks The keyword "VERL" is the opposite of "LANG", not the opposite of "LEAP". The documentation implies this, but it is poorly written. This problem causes the old integrator to be used when it shouldn't. Files modified: source/dynamc/dcntrl.src .............................................................................. (2) Default target temperatures for dynamics - Bernard R. Brooks Change the default of TBATH from 0.0 to FINALT Change the default of TREF from ROOMT to FINALT Change the default of RTMPR from ROOMT to FINALT Files modified: source/dynamc/dcntrl.src .............................................................................. (3) 4-D Implicit Euler integration code - Bernard R. Brooks Implicit Euler integration code has been removed from 4-dimensional method. It wasn't implemented properly. Files modified: source/dynamc/dcntrl.src /dynamc4.src .............................................................................. (4) Heap memory reduction to QM/MM code (MOPAC version) - Bernard R. Brooks Files modified: charmm/miscom.src quantum/qmene.src .............................................................................. (5) Rename of ALP in the QM code - Bernard R. Brooks ALP has been renamed ALFA to avoid a naming conflict with the variable ALP in param.fcm. Files modified: source/fcm/am1parm.fcm /quantum/qmdata.src /qmene.src /qmset.src .............................................................................. (6) IATMXB for Replica - Bernard R. Brooks Fixed a bug in defining IATBMX when replicas are bound to non-replicated atoms. I found a compromise that hopefully satisfies all needs. This could be done better by counting the bonds to each atom when replicas are in use. Files modified: nbonds/nbexcl.src .............................................................................. (7) ICFIX with the leap-frog integrator - Bernard R. Brooks The ICFIX methods are now supported in both the old and the leap-frog integrator. Files modified: source/dynamc/dynamc.src .............................................................................. (8) Graphics parsing improved - Bernard R. Brooks ##IF IRIS ; ##IFN XDISPLAY is changed to ##IF GLDISPLAY Files modified: source/charmm/charmm.src .............................................................................. (9) Old integrator and Parallel Compatibility - Bernard R. Brooks It is now possible to have a single executable support both parallel methods and the old integrator. Note, the old integrator will not run in parallel. Files modified: source/dynamc/dynamcv.src .............................................................................. (10) Parallel bug in the ENERGY command when SHAKE is used - Bernard R. Brooks The call to VDGBR (global broadcast) in the ENERGY command was poorly placed and caused errors in the force calculation when SHAKE was turned on. A simple modification fixes the problem. Files modified: source/energy/eutil.src .............................................................................. (11) Bug in QM/MM parsing - Bernard R. Brooks There was a bug in the use of the subroutine FINDEL for QM/MM using GAMESS. The incorrect RTF array was used for element identification that can cause errors. Files modified: source/gamint/gamini.src /quantum/addlnat.src /qmset.src .............................................................................. (12) Error processing in Hbonds - Bernard R. Brooks An error message has been added in the routine HCODES. Files modified: source/gener/update.src .............................................................................. (13) Format error in parallel code - Bernard R. Brooks Files modified: source/machdep/parset.src .............................................................................. (14) Compatibility between TNPACK and GAMESS - Bernard R. Brooks Several routines in TNPACK were the same as those needed to GAMESS. The duplicate routines are now removed from the TNPACK code is the GAMESS compile flag is enabled. Files modified: source/minmiz/tnpack.src .............................................................................. (15) Jump into an IF block - Bernard R. Brooks The line labeled 180 was placed inside of an IF block in NBONDG. Some compilers object when code jumps into an IF block. Files modified: source/nbonds/nbondg.src .............................................................................. (16) CALC error - Bernard R. Brooks A problem of error handling in calc is fixed. Files modified: source/util/calc.src .............................................................................. (17) Non-bonded exclusions for replicas (B960206.clb) - Charles L. Brooks, III Non-bonded exclusions for replicas done incorrectly in cnbnd.src. Files modified: source/nbonds/cnbnd.src .............................................................................. (18) Vectorization on C90 (R960129.clb) - Charles L. Brooks, III 1. vectorized energy/cenerf.src, new dihedral calculation was not vectorized. 2. ivdep added to image/upimag.src 3. nbonds/nbonds.src changed to use vector routine if crayvec or parvec in pref.dat Files modified: source/energy/cenerf.src /image/upimag.src /nbonds/nbonds.src .............................................................................. (19) T3D code fixed (R960129.clb) - Charles L. Brooks, III 1. rewrote psndc, psnd4, psnd8 in machdep/parallel.src to be more efficient, current routines fail on large machines. 2. rewrote t3d startup stuff in machdep/cstuff.c to use environment variables for startup configurations. 3. increased HEAPDM in fcm/heap.fcm 4. changed MAXSHK in fcm/dimens.fcm, PARAMETER (MAXSHK = SIZE*3/4) 5. changed util/cmdpar.src to add t3d work around. 6. commented out redundant code in machdep/machutil.src, compiler won't compile same routine twice! 7. rewrote psync in machdep/parallel.src to use hardware barriers 8. removed call to shell in graphics/apograph.src, not a supported system call on the t3d. 9. removed synchron from pref.dat. files modified: source/machdep/parallel.src /machutil.src /cstuff.c /fcm/heap.fcm /dimens.fcm /graphics/apograph.src .............................................................................. (20) U-B term is added for TSM (R960129.clb) - Charles L. Brooks, III Added code to permit Urey-Bradley energy terms to be computed. Files modified: source/pert/tsms.src /tsme.src /fcm/tsmh.fcm .............................................................................. (21) Bugfix for MPI version on SPP1000 (R960129.clb) - Charles L. Brooks, III Files modified: source/machdep/parallel.src .............................................................................. (22) FMTMX increase (R960129.clb) - Charles L. Brooks, III changed parameter FMTMX=8 to FMTMX=50 to accommodate a larger number of translate commands. Files modified: source/fcm/univ.fcm .............................................................................. (23) Error in allocation of tasks to specific cpu's (R960129.clb) - William A. Shirley and Charles L. Brooks, III Calculation of the restraint energy terms which use the normal internal energy functions were being performed incorrectly on parallel machines because work was being partitioned among processors both in energy and at the loop level in the internal energy routine itself. The problem meant that only part of the restraint energy would be computed. The fix was to remove the processor partitioning of these energy terms at the level of the subroutine call. Files modified: source/energy/energy.src .............................................................................. (24) Parallel logic error (GRECSEN) (R960129.clb) - William S. Young and Charles L. Brooks, III At the top of subroutine GRECSEN the code probes for a message and receive the message if present. later in the code, the code probes and loops looking for a message, if the message has already been received it can not be received a second time causing an infinite loop. Files modified: source/machdep/parallel.src .............................................................................. (25) Non-functional parallel code on clusters with socket option (B950817.ln) - Lennart Nilsson The job immediately crashes because the slaves get an "UNRECOGNIZED COMMAND" error in the charmm command parser. Adding ##ELIF SOCKET fixes the problem. Files modified: source/machdep/parallel.src .............................................................................. (26) Excessive f.p. underflow messages from DEXP (B950823.rv) - Rick Venable The RISM testcase generates numerous error messages about f.p. underflow errors occurring within DEXP, when compiled with the +T command line flag for the compiler. The flag suppresses core dumps and generates a traceback instead, but also turns off the default f.p. trap routines. Trap routines were added which handle any underflows in code, but these don't apply to external functions such as DEXP. Files modified: source/machdep/startup.src .............................................................................. (27) SHAKE crashes when PERT is being used with TIP3 (B950914.br) - Benoit Roux To incorporate the influence of bond length changes in PERT, the SHAKE code was modified in c24b1 (relative to c24a3). It turns out that problems can be encountered, even in cases in which no bond length is being perturbed. For example, in perturbation of a solute in the presence of TIP3. The origin of the problem has now been traced to the subroutine REAL*8 FUNCTION PTARGET(IX,JX,DERI) (in /source/manip/shake.src). The reason is that a "Lambda-dependent" shake constraint is setup even where the value of CONSTR(NCONST) (the bond length squared) is set to PTARGET={(LAMDAM*KOLD*ROLD+LAMDA*KNEW*RNEW)/(LAMDAM*KOLD+LAMDA*KNEW)}**2 Normally, if ROLD=RNEW, the expression should give back the good old CONSTR(NCONST), but there are obvious problems with TIP3 because the H1-H2 distance has a zero force constant. Files modified: source/manip/shake.src .............................................................................. (28) QNOROT (B951002.clb) - Zhongxiang Zhou, Charles L. Brooks, III It seems that the bugfix B950501e.sb done on dcntrl.src is a bug itself. QNORT = .TRUE. means no translation or rotation. QALWRT = .TRUE. means the opposite. Hence, QNORT(I) = .TRUE. should leads to QALWRT(I) = .FALSE. Files modified: source/dynamc/dcntrl.src .............................................................................. (29) Dimension problem for NA-Protein energy calculations - Jianpeng Ma, Lennart Nilsson Program crashes or gives erroneous energies, or other errors upon energy calculations with combined parameter files (protein:dna, protein:lipid). The problem is due to the dimensional relations between parameters MAXCUS, MAXCN and MAXCNB, which were not properly observed. MAXCUS=128 is sufficient and MAXCN=20000 is also sufficient (has to be .GE. MAXCUS*MAXCUS) but with a recent increase in MAXCUS from 100 to 128 MAXCNB was no longer sufficient at 20000 MAXCNB=40000 works (should be 2*MAXCN, which is also stated in dimens.fcm). Minimal checking and a error message are added in MAKITC of nbexcl.src. Files modified: source/fcm/dimens.fcm /nbonds/nbexcl.src .............................................................................. (30) CUTA option of HBALAL - Lennart Nilsson The angle cutoff option in the coor hbonds module is fixed. Files modified: source/manip/hbanal.src .............................................................................. (31) Fixes for OS2 port - Stefan Boresch Problems with REWIND and DCMPLX on PCs are corrected. Files modified: source/dynamc/dynio.src /machdep/machio.src /minmiz/tndriv.src tnpack.src /misc/nmr.src ssbp.src .............................................................................. (32) Divide by zero error - Jay L. Banks Floating point exception (divide by zero) occurs if no atoms selected. Add zero-checking of AMASST in the STAT command section. Files modified: source/manip/corman.src .............................................................................. (33) Array name correction - Ryszard Czerminski iRepID = repNoA(iRepNo) is misspelled, should be repID(iRepNo). Files modified: source/nbonds/nbndf2p.src .............................................................................. (34) Max logical unit - Ryszard Czerminski Parameter MAXUN is set to 99 for all systems. Files modified: source/fcm/iochan.fcm =========================================================================== [2] c25a2 Change Log CHARMM c25a1 (February 15, 1996) to c25a2 (August 15, 1996) 2.1 NIH Development - Bernard R. Brooks, Scott Fellar, Milan Hodoscek and others at NIH 2.1.1 MMFF Reorganized The MMFF code has been modified so that the structure of the CHARMM binary parameter file is unaffected by the MMFF compile flag option. Several other changes were made to correct for other problems with the MMFF implementation which include: - Removal of the MMFF specific FAST option (not needed). - Generalization of the USE command (not just for MMFF). - Elimination of the setting of SKIP flags in the USE command. - Only the SKIP command may modify the SKIP flags. - The MMFF routines were grouped as suggested by Tom Halgren. Files added: source/mmff/assignpar.src, datastruc.src, efast_mm.src, enbfast_mm.src, enbscalar_mm.src, escalar_mm.src, merckio.src, misc_mm.src, mmff.src, mmfftype.src, parse_mm.src, readpar.src, unused_mm.src Files removed: soruce/mmff/*.src Files modified: source/charmm/iniall.src, miscom.src energy/eutil.src, intere.src, printe.src fcm/auxpar.fcm, consta.fcm, deflts.fcm, energy.fcm, fast.fcm, ffield.fcm, io.fcm, mmff.fcm misc/testch.src nbonds/nbutil.src pert/block.src, epert.src 2.1.2 Shape Descriptor Code A new shape descriptor facility has been developed for shape analysis structure matching based on shape, QSAR, and for docking. There is also a restraint energy term based on how well a flexible molecule fits a shape or how well two flexible molecules can adopt a similar shape. Note: This code is still under development. Files added: source/shapes/mdlio.src, shapes.src fcm/shapes.fcm Files modified: source/energy/eutil.src, printe.src fcm/energy.fcm io/mainio.src minmiz/steepd.src (Note) This code was withdrawn by Bernard R. Brooks as of August 2, 1996, * during the circulation period of the c25a1a developmental intermediate * version. All modifications except the newly introduced files, * shapes/mdlio.src and shapes/shapes.src, are retained for future * development. It is an exception. No code can be checked in unless * it is fully developed and validated. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 2.1.3 Extension of Particle Mesh Ewal Code The Particle Mesh Ewald (PME) method has been implemented and revised. The primary enhancement is the ability to run in parallel. We have also fixed another bug in the pressure calculation that caused an error of approximately 10 atmospheres. The new code from Mike Crowley is in there, with the communication scheme Milan came up with. There is a bug which causes the restriction that mod(fftz,numnod)=0 or numnod -1. So everything works with 1 or 2 nodes but with 4 nodes some values of fftz are not allowed. We are trying to fix this bug. Files added: source/fcm/pme_par.fcm Files modified: source/charmm/iniall.src energy/energy.src nbonds/pme.src 2.1.4 Pressure Update Scott cleaned up a bunch of code that was hanging around from testing and removed some junk variables that weren't being used. He also fixed a bug that occured when a nonzero PGAMma was used with ISOTropic pressure scaling. Files modified: source/dynamc/prssre.src fcm/reawri.fcm 2.1.5 New Time Series in Correl Scott added a new time series, INERtia, to the principal axis of an atom selection Files modified: source/correl/anacor.src, correl.src 2.1.6 Restrained Distance Code Enhancement The restained distance method has been extended to allow the use of a one sided function (positive or negative). It also allows a non-unit exponent for the individual distance terms. The code is now much more general in its ability to define distnace based retraints based on multiple distances. Files modified: source/energy/energy.src fcm/resdist.fcm misc/resdist.src 2.1.7 GAMESS Interface Code Enhancement The GAMESS code will no longer do a single point QM energy evaluation when invoked. It just sets up the QM part and awaits further commands. Files modified: source/gamint/gamini.src fcm/gamess.fcm misc/zmat.src 2.1.8 COOR DIPOLE A COOR DIPOle command has been added. This command computes tha charge and dipole (multipoles) for selected atoms. Files modified: source/manip/corman.src fcm/consta.fcm 2.1.9 READ PSF APPEnd The READ PSF APPEnd command option has been modified so that it does not initialize the coordinates of existing atoms. Only the new appended atoms will have undefined coordinates. Files modified: source/io/mainio.src 2.1.10 Replica within Images The replica code has been enhanced so that it workes with images and the crystal facility. Files modified: source/image/nbondm.src 2.1.11 Space Allocation Some problems with unnecessary or incorrect use of space allocation was corrected. The unused routine INTEG2 has been removed. Files modified: source/dynamc/dcntrl.src fcm/dimens.fcm, heap.fcm, tbmts.fcm machdep/space.src 2.1.12 Parallel Update The parallel code has been updated. The new code is faster and there has been a significant additions to support other platforms. We now support about 15 platforms. Files added: source/machdep/paral1.src, paral2.src, paral3.src Files removed: source/machdep/parallel.src Files modified: source/machdep/parset.src, socket.c image/upimag.src rxncor/rxndef.src 2.1.13 Terra Code New code has been added to support the new multiprocessor Terra system. Files modified: source/machdep/cstuff.c, machio.src, machutil.src, startup.src 2.1.14 Graphics Update Files modified: source/graphics/apodraw.src, apograph.src, graphx.src, iris_graphics.c machdep/xdisp.c 2.1.15 Code Protection A number of changes are made regarding code protection using ##IF's. Since most code specific common block contain internal ##IF's, it is not necesary to protect the ##INCLUDE line. For example, in charmm.src, ##IF MTS ##INCLUDE '~/charmm_fcm/tbmtsp1.fcm' ##ENDIF is changed to: ##INCLUDE '~/charmm_fcm/tbmtsp1.fcm' There are also several cases where the code protection was inserted in the wrong place and there are instances where code protection is added. Finally, protection to parsing has been removed in several cases and replaced with an error messag in the target subroutine. For example, in charmm.src, ##IF GAMESS ELSE IF (WRD.EQ.'GAME') THEN CALL GAMINI(COMLYN,COMLEN) ##ENDIF has been changed to: ELSE IF (WRD.EQ.'GAME') THEN CALL GAMINI(COMLYN,COMLEN) And an error message has been added to GAMINI when the GAMESS code is not compiled. Files modified: source/charmm/charmm_main.src, iniall.src dynamc/mts.src energy/energy.src fcm/fmacons.fcm, polymer.fcm, selcta.fcm gener/genpsf.src, modpsf.src, update.src nbonds/enbfast.src, enbond.src, heurist.src, nbondg.src pert/pert.src 2.1.16 iniall.src Reordered The code in iniall.src was reordered so that the include files are processes alphabetically. Files modified: source/charmm/iniall.src 2.1.17 Trajectory Option Parsing Default trajectory parsing has been corrected so that the default options are consistent. The default BEGIn value is now 0 (zero) indicating that the first available frame will be used. CHARMM is now consistant in this regard. The use of BEGIN=1 where it is not possible will result in an error message. Files modified: source/correl/clustr.src rxncor/travel.src 2.1.18 Rename The subroutine CENMAS was renamed CENMSS to avoid a naming conflict in GAMESS. Files modified: source/dynamc/dynutil.src 2.1.19 Indentation and Other Cosmetic Stuff Some files were modified so as to be easier to read. This also includes fixing spelling errors. Source files were modified so that the END is on the last line (some compilers have trouble with extra lines). The .fcm files were modified so as to end in a consistent manner. Files modified: source/dynamc/dynamc.src, dynamvv.src fcm/block.fcm, epert.fcm, etable.fcm, excl.fcm, exfunc.fcm, fft.fcm, fma.fcm, fshake.fcm, graph.fcm, graphdep.fcm, nbndqm.fcm, noe.fcm, number.fcm, path.fcm, pbeq.fcm, pert.fcm, pshake.fcm, qcommon.fcm, quanta.fcm, quantm.fcm, replica.fcm, rism.fcm, rxncom.fcm, sbound.fcm, sizes.fcm, solana.fcm, struc.fcm, surface.fcm, vangle_mm.fcm, vphi.fcm image/crystal.src, eimage.src, manip/cstran.src misc/pbeq.src nbonds/nbonds.src util/vector.src 2.1.20 Minor problems Several minor problems have been fixed (code location, missing SAVE, use of ZERO, parameter parsing). Files modified: source/manip/corman3.src minmiz/nraph.src quantum/qmpac.src util/cmdpar.src ------------------------------------------------------------------------------ 2.2 Developments at the Scripps Research Institute - Charles L. Brooks, III 2.2.1 The DMAT Command Files modified: source/manip/corman2.src doc/corman.doc miscom.doc 2.2.2 Cray Code Clean-up UNICOS is replaced by CRAYVEC for preprocessing. MAXCPU is increased to 16 from 8 in machdep.fcm. Files modified: source/charmm/iniall.src fcm/machdep.fcm manip/shake.src 2.2.3 cstuff.c cstuff.c is cleaned and organized. Done by Bill Young and Milan Hodoscek. Files modified: soruce/machdep/cstuff.c ------------------------------------------------------------------------------ 2.3 External Force to Selected Atoms - Lennart Nilsson A new command has been added which calculates a new energy term corresponding to a static or periodically varying external force on an atom selection. For a full description see new section in cons.doc. Files Added: source/energy/pull.src fcm/pull.fcm test/c25test/pull.inp Files Modified: source/charmm/charmm_main.src, iniall.src dynamc/dynamc.src energy/energy.src, eutil.src, printe.src fcm/energy.fcm doc/cons.doc ------------------------------------------------------------------------------ 2.4 DIMB Enhancement - Herman van Vlijmen Fixed atoms can now be present in a normal mode calculation with VIBRAN. Atoms should be fixed with the CONS FIX command. Instead of the standard DIAG command in VIBRAN, the command REDU FIX should be used to take the fixed atoms into acount. The use of the compressed second derivative matrix is supported through use of the CMPAct keyword. The BIG option is added to the DIMB command in VIBRAN. For the initial basis calculation, which can be done separately by specifying ITER=0, a big portion of the memory space is saved by specifying BIG. This will write an intermediate vector basis temporarily to disk, instead of keeping it in memory. Files Modified: source/vibran/vibran.src, redbas.src dimb/nmdimb.src, dimbsub.src, dimbutil.src doc/vibran.doc test/c24test/dimb1.inp, dimb2.inp ------------------------------------------------------------------------------ 2.5 TRAVEL Update - Stefan Fischer 1. The CPR command has been made compatible with the QM/MM energy options in CHARMM. See the new TRAVEL.DOC for a description of the re-optimized CPR parameters to be used in that case or when the energy function and its gradient are non-analytical. 2. Coordinate-scaling has been added to all commands of the module. It allows to put different weights on the motion of selected atoms. This allows to "stretch" the potential-energy surface along those coordinates which contribute a lot to a reaction. This can be usefull for QM/MM calculations, where the energy surface is very anisotropic, i.e. large energy changes over very small displacements for only a few of the atoms treated quantum-mechanically. 3. The CPR command is more robust than before. Specifically, when the computer reaches machine-precision during the search of a saddle-point, which is likely when more than 1000 atoms are moving, this condition is recognized and no CPU time is wasted. The tentative saddle-points are flagged accordingly. 4. The CPR command allows to specify a reference coordinate-set upon initialization, which serves for coordinate reorienting of new path-points, rather than always using the 1st point of the read-in path for that purpose. This allows to split partially refined reaction-paths, so that their refinement can be continued simultaneously on several CPUs and/or so that the memory requirements can be kept low. 5. Better control over the CPU usage of a CPR run by specifying the total number of energy calls per run, rather the number of CPR cycles (specially useful for calculations performed at Supercomputing Centers). Files Modified: source/fcm/travel.fcm rxncor/travel.src doc/travel.doc ------------------------------------------------------------------------------ 2.6 Developments at University of Montreal - Benoit Roux, Dmitrii Beglov, Konrad Hinsen 2.6.1 Polarizable Water Model We have introduced the dissociable/polarizable water model PM6 of Stillinger-David-Weber in part into CHARMM. This is completely independent of the energy function and allows to protonated species and proton transfer in water. IMAGES are not supported. The path integral will be suported. Files added: source/energy/polar.src fcm/polar.fcm doc/polar.doc test/c25test/pm6test1.inp Files modified: source/charmm/charmm_main.src, iniall.src energy/energy.src, eutil.src, printe.src fcm/energy.fcm 2.6.2 PBEQ Update A set of newly parametrized atomic radii for electrostatic free energy is incorporated as a stream file. Files modified: source/misc/pbeq.src fcm/pbeq.fcm 2.6.3 Finite Differentiation in MANTIM A finite difference first derivative is added. Files modified: source/correl/mantim.src doc/correl.doc ------------------------------------------------------------------------------ 2.7 Bugfixes (1) Analysis Printout Bug - Bernard R. Brooks There was a bug in the printout from the ANALysis. Files modified: nbonds/enbond.src (2) Preprocessing Error Fix - Charles L. Brooks, III Fixed compile problems. When MTS not specified in pref.dat there is a compilation error due to inappropriately protected variables. FMA is also added in nbutil.src. Files modified source/dynamc/mts.src nbonds/nbutil.src (3) Formatting Trajectories on Parallel Machines - Lennart Nilsson Files modified: source/dynamc/dynio.src (4) Timing Routine of IBMSP - Lennart Nilsson RTC is used for timing of IBMSP. Files modified: source/machdep/parallel.src - The change is incorporated into paral3.src. (5) Loop Index Error - Boryeu Mao (bmao@upj.com): B960605.bm There is a coding error in the section that finds "holes" for the -Z pass. Files modified: source/manip/corman2.src (6) EXSG Option for GROUP - Ryszard Czerminski: B960628.rcz EXSG option does not work with GROUP list. Files modified: source/nbonds/nbondg.src gener/update.src - The trap was removed in the past. (7) RDNEXCO Trajectory Reading - Matthias Buck: B960710.mb The array FREEAT is used for reading trajectory files which contain fixed coordinates (lines 1992-1996: RDHEAD) later handeled by RDNEXCO (lines 1900-1912). However, program crashed at line 1903 because FREEAT had not been transmitted to the subroutine RDNEXCO. Files modified: source/correl/solana.src (8) Parsing Error of WHAM - Youngdo Won Command parsing keywords are fixed in accordance with the documentation. Files modified: source/pert/wham.src =========================================================================== [3] c25a3 Change Log CHARMM c25a2 (August 15, 1996) to c25a3 (February 15, 1997) 3.1 NIH Developments - Bernard R. Brooks 3.1.1 Nonbond overhaul The nonbond energy calculation and list generation section of CHARMM are overhauled. This is a major overhaul involving nearly every routine and file related to van der Waal and electrostastics. More than 20,000 lines of source code has been removed, but yet the code has more options and it runs faster. The development in summary: - Enhanced the use of combinations of methods (e.g. EWALD with MMFF) - Error messages when unsupported combinations are used - Heavy use of semi-automatic code expansion - Cascade of fast routine selection in ENBOND - vestigial code removed - ERFC tables (for Ewald) inlined for speed using a cubic spline - ZTBL code removed - QEWEX code is removed (also IEWEX,JEWEX,...) - RXNFLD and EXELEC enabled - Combined group and atom based nonbond list routines split. - Assorted bugs found and fixed Files added: source/nbonds/enbonda.src (new - from enbond.src) /nbonds/enbondg.src (new - from enbond.src) /nbonds/nbonda.src (new - from nbondg.src) Files removed: source/nbonds/enbf3.src /nbonds/enbf4.src /nbonds/enbf5.src Files modified: source/fcm/dimens.fcm /fcm/psf.fcm /image/upimag.src /image/cnbndm.src /image/imnbfp.src /mmff/enbfast_mm.src /mmff/enbscalar_mm.src /nbonds/cenbf.src /nbonds/enbf2.src /nbonds/evdwf.src /nbonds/ewaldf2.src /nbonds/nbexcl.src /nbonds/nbndgc.src /nbonds/nbondg.src /nbonds/nbonds.src /nbonds/nbutil.src /nbonds/pme.src .............................................................................. 3.1.2 Z-table (ZTBL) code removed. All ZTBL code has been removed. This code was unnecessary and caused problems. Without it, the code uses less memory and runs faster. Files removed: soruce/nbonds/ztbl.src Files modified: source/fcm/dimens.fcm /fcm/psf.fcm /image/upimag.src /nbonds/nbexcl.src /nbonds/nbndgc.src .............................................................................. 3.1.3 Semi-automatic code expansion The program PREFLX (or PREFX) has been overhauled to allow semi-automatic code expansion in the moving of inner loop if-tests to the outside of do-loops. The program has also been enhanced to allow: ##ELIF .not.FLAG - Allows using the complement of a flag ##SET flag - Allows the local setting of flags at the current level ##SET .not.flag - Allows the local removal of flags at the current level ... !##PERT - One line conditional processing ... !##PERT !##MMFF - A one line "AND" conditional compile ... !##PERT MMFF - A one line "OR" conditional compile Files modified: tool/prefx.src /prefx.f .............................................................................. 3.1.4 Energy term routine selection Energy term selection control has been been removed from ENERGY. There is a new module energy/ecntrl.src that controls which internal energy term routine will be called. Also, the selection for the appropriate MMFF routine is also contained therein. This greatly simplifies ENERGY and allows other energy based routines (PERT, EINTERN,..) to use the fast options in a straightfoward manner. Files added: source/energy/ecntrl.src Files modified: source/energy/energy.src /energy/eintern.src /gener/makphi.src /pert/epert.src .............................................................................. 3.1.5 Energy term usage The establishment of the new energy terms, DMC and RGY was suboptimal. There should be no ##IFs in the file fcm/energy.fcm relating to energy term definitions. Also, the routine ENERIN was updated to give these terms names so that the SKIP command can be used. The subroutine PRINTE was updated to give specific entries for the energy terms: RESTR> CDROplet EHARmonic SHAPe DMC RGY The energy term, EPULL, was added to the line "POLAR>" The only terms without specific entries (still lumped into EOTHER) are: ST2 and IMST2. Files modified: source/fcm/energy.fcm /energy/eutil.src /energy/printe.src .............................................................................. 3.1.6 EWALD with MMFF A version of EWALD was developed for MMFF. The usual MMFF electrostatic term: qq/(r+d) is split into two terms: qq/r - qq*d/(r*(r+d)) The first term is handled by the Ewald method in the usual manner (real-space and k-space parts) and the second term is truncated at the cutoff distance using a switching function (from CTONNB to CTOFNB). Since the second term is quite small at the cutoff distance, the use of a switching function should not introduce significant artificial forces. In the processing of testing the new code, I fixed a few problems with the k-space sum (PARVECT version) for the calculation of pressures. Files modified: source/mmff/enbfast_mm.src /mmff/enbscalar_mm.src /nbonds/ewaldf.src /nbonds/ewaldf2.src .............................................................................. 3.1.7 Update to EWALD code The calling sequence to ENBOND was modified so that a flag (QEWEX) can be sent indicating whether the nonbond exclusion correction should be performed for the Ewald calculation. This corrects several problems (such as Ewald with MTS and Ewald with PERT) and this simplifies some code relative to the handling of the exclusion lists. Also there were several changes to EPERT so that the Ewald method will report a correct internal virial (for pressure). The Ewald method was enabled for the GROUP option so that group lists can be used. This reduces the amount of memory and the time needed to handle the nonbond lists (good for limited memory parallel machines). Files modified: source/energy/intere.src /fcm/ewald.fcm /image/eimage.src /mmff/enbfast_mm.src /nbonds/enbond.src /nbonds/enbondg.src /nbonds/evdwf.src /nbonds/nbonds.src /nbonds/nbutil.src /pert/epert.src /pert/icpert.src /pert/tsme.src .............................................................................. 3.1.8 Dodecahedal symmetry in CRYSTAL Benoit's new doedecahedral code for the crystal facility is added with some minor corrections. Files modified: source/image/eimage.src /image/crystal.src .............................................................................. 3.1.9 Crystal Build rotation "feature" removed The new crystal build "feature" of rotating the coordinates from an aligned to a symmetric frame has been removed. Although such a rotation is necessary when starting with aligned coordinates, this is the wrong way to do it. The COOR CONVert command has been enhanced (by Ryszard Czerminski) to properly handle this operation. The routine INCRYS has been moved to the end of the file (outside of the ##IF NOIMAGES). A new routine XTLMSR have been added which sets substitution variables. The routine SETXTL and GETXTL have been moved to crystal.src Files modified: source/image/crystal.src /manip/corman.src /manip/corman2.src /minmiz/abner.src /minmiz/egrad1.src /minmiz/nraph.src /minmiz/powell.src /minmiz/tnpack.src /util/array.src .............................................................................. 3.1.10 Crystal information processed on READ COOR The READ COOR command now proceeses the crystal information on reading. Files modified: source/io/coorio.src .............................................................................. 3.1.11 Coor CONVert fixed Changes (from Ryszard Czerminski) needed to get the COOR CONVert command to work properly were added. Several matrix utility routines are added to util/matrix.src and the parsing was fixed. Files modified: source/manip/corman.src /util/matrix.src .............................................................................. 3.1.12 PBOUND in CRAY nonbond routines. The PBOUND code was added to the EXPAND sections of CENBF. This should enable the used of PBOUND on the Cray without affecting its performance when PBOUND is not used. In order to limit the size of this routine (to less than 6000 fortran lines), the NOFORCE option within BLOCK has been disabled and this function is now handled in the other fast routines (ENBF, ENBFS8, ENBFV8) or in the improved slow routine (EVDW). The PBMOVE call is disabled (as it was in the recent code from SRI) without testing or error message (so... user beware - until we fix this). Files modified: source/nbonds/cenbf.src .............................................................................. 3.1.13 Use of properties for atoms selection enhanced The property syntax for atom selection has been extended. All old input scripts should continue to work as before. The new construct avoids the need to copy the desired array into WMAIN before using "PROP 1". The new syntax is: PROPerty [ABS] <.LT.|.GT.|.EQ.|.NE.|.GE.|.LE.|.AE.> The allowed strings are: "1" and "1" - The active weighting array (WMAIN or WCOMP) (This old construct works only when properties are actually present) keyname - An array keyname (see scalar.doc) of: X Y Z WMAIn XCOMp YCOMp ZCOMp WCOMp DX DY DZ ECONt EPCOnt MASS CHARge CONStrai XREF YREF ZREF FBETa MOVE TYPE IGNOre ASPValue VDWSurfa ALPHa EFFEct RADIus Examples: print coor sele prop abs charge .gt. 0.5 end print coor sele prop radius .gt. 3.0 end Files modified: source/util/selcta.src .............................................................................. 3.1.14 DATE command added There is now a DATE command which prints the current date and time. Files modified: source/charmm/miscom.src .............................................................................. 3.1.15 COOR HELIX command enhanced The output from the COOR HELIX command is enhanced. Files modified: source/manip/helix.src .............................................................................. 3.1.16 SCALAR RANDOM The SCALAR command has been enhanced to allow the generation of random arrays. Also, the SCALAR STAT command now prints the variance of the selected data and puts it into the variable ?SVAR. Files modified: source/manip/scalar.src .............................................................................. 3.1.17 Room temperature Room temperature, 298K, is now a general default. Other temperatures follow the specification of FINALT (i.e. when you specify FINALT, this becomes the default for ALL other temperature specifications). The use of different defaults for temperatures specifications has led to some interesting problems. The HOOVER CT parsing has been moved from prssre.src to dcntrl.src Files modified: source/charmm/iniall.src /dynamc/dcntrl.src /dynamc/prssre.src .............................................................................. 3.1.18 Bugs in NONBOND fast routines. CNBNDM was enhanced so that it can be tested on scalar machines. A bug in CNBNDM when LIMALL is used was found and fixed. A related bug in IMNBFP was also fixed. Files modified: source/image/cnbndm.src /image/imnbfp.src .............................................................................. 3.1.19 Bug in CORREL CORFUN A bug was found in the CORREL CORFUN command that caused wrong answers was discovered. This was due to not initializing an array. Also, and "IF" test was wrong for the selection of P@ by direct manipulation. Files modified: source/correl/corfun.src .............................................................................. 3.1.20 MMFF problems A number of changes have been made to correct problems with MMFF. - Declaration of estar and rstar increased to maxcn*2 - GENERATE segid DUPLicate ... command fixed. - replace SAYC with calls to WRNDIE where appropriate Files modified: source/fcm/param.fcm /gener/genpsf.src /mmff/assignpar.src .............................................................................. 3.1.21 REPLICA problems The handling of the IC table in REPLICA wasn't exactly correct. A waring message has been added if PERT is invoked before REPLICA to make sure that they must be used together in the correct order. Files modified: source/gener/replica.src .............................................................................. 3.1.22 Atom number added to labels in graphics Atom numbers may now be displayed using CHARMM graphics. Within the LBL command, the keywords ATNU or ATNO enable this feature. Files modified: source/graphics/graphx.src .............................................................................. 3.1.23 Cleanup of dynamc/dynio.src The new routines WRITLB, WRILDY and REALDY were moved to the end of file. Recent image code added to READYN was also applied to REALDY. The new code in routines WRILDY and REALDY should be folded into the parent routines READYN and WRIDYN (and these routines removed). Files modified: source/dynamc/dynio.src .............................................................................. 3.1.24 Move ADDLTOU The routine ADDLTOU was moved from mmff/escalar_mm.src to util/matrix.src. It is now another general utility routine. The file mmff/unused_mm.src is removed (since none of its routines are used). Files modified: source/mmff/escalar_mm.src /mmff/unused_mm.src /util/matrix.src .............................................................................. 3.1.25 DIAGQ resolution A ##IF CRAY section has been added to DIAGQ in an attempt to resolve the problems with this routine on CRAY vs. non-CRAY platforms. This one line change will hopefully solve this (but needs testing). Files modified: source/util/diagq.src .............................................................................. 3.1.26 Comments Comments were added or fixed in several files. Some of this is still incomplete (e.g. fcm/tbmts.fcm). REMEMBER: ALL variables in ALL include files need to be commented! Files modified: source/dynamc/dynio.src /fcm/tbmts.fcm /misc/aspener.src /misc/resdist.src /nbonds/heurist.src .............................................................................. 3.1.27 MARK value changed In many routines, the integer MARK value was be set to -9999. In systems with more than 9999 atoms, this lead to problems because the negative pointers are sometimes used as flags. The standard integer MARK value has been reset to -99999999 (1-10**8) to avoid this problem. Files modified: source/correl/correl.src /dimb/nmdimb.src /gener/genpsf.src /gener/hbonds.src /gener/modpsf.src /image/images.src /io/coorio.src /io/univio.src /manip/intcor.src /pert/pert.src /util/chutil.src /vibran/vibran.src .............................................................................. 3.1.28 CHARACTER*4 for arrays Use of CHARACTER*4 rather than CHARACTER*(*) for character arrays removed some problems with a rogue F77 compiler. Files modified: source/correl/correl.src /correl/corrio.src .............................................................................. 3.1.29 ##IF code protection The preprocessor directives were added and/or modified in several routines. Files modified: source/dynamc/prssre.src /energy/polar.src /pert/icpert.src /fcm/impnon.fcm .............................................................................. 3.1.30 More parallel code Parallelization of more code: - READCV, FOURD - Restrained Distances (RESD) (actually, parallel bug fixed) - Parallel code has been added to EPERT Files modified: source/dynamc/dynio.src /machdep/paral1.src /pert/epert.src /pert/pert.src .............................................................................. 3.1.31 PRNLEV and WRNLEV commands enhanced There is now a NODE option to these commands to aid in debugging with parallel processing. For example, the sequence; PRNLEV -1 PRNLEV 6 NODE 4 will shutoff the normal print and then have only node 4 print. Files modified: source/charmm/miscom.src .............................................................................. 3.1.32 Use of WRNDIE Several calls to CALL DIE and CALL DIEWRN have been replaced with calls to WRNDIE Files modified: source/correl/cordyn.src /graphics/drawit.src .............................................................................. 3.1.33 Freeing HEAP space CHARMM should free all space at the termination of a run. This helps find problems with new code. Several calls were added to free "permanent" HEAP space. Files modified: source/charmm/iniall.src .............................................................................. 3.1.34 WRNLEV vs. PRNLEV There were a number of printed warnings that used PRNLEV instead of WRNLEV to trap. I made appropriate adjustments. Some tests for IOLEV are also included. Some omitted I/O tests we added (e.g.TNPACK). Files modified: source/charmm/miscom.src /graphics/drawit.src /minmiz/tnpack.src /mmff/assignpar.src /mmff/escalar_mm.src .............................................................................. 3.1.35 Vestigial code removed Some unused old code was removed. - DPCOMM specification - READCV4 and WRITEC4 - Removal of unused local variables Files modified: source/charmm/miscom.src /dynamc/dynio.src /nbonds/enbfast.src.diff ------------------------------------------------------------------------------ 3.2 TSRI/PSC Developments - Charles L. Brooks, III 3.2.1 Lambda dynamics Incorporated James Kong's lambda dynamics and asymmetric block interaction matrix for docking. New keywords for pref.dat LDM and DOCK. (CLB/XK) Files added: source/fcm/lambda.fcm /fcm/rwlamb.fcm Files modified: source/charmm/iniall.src /charmm/miscom.src /dynamc/dcntrl.src /dynamc/dynamc.src /dynamc/dynamcv.src /dynamc/dynamvv.src /dynamc/dynio.src /energy/eintern.src /energy/enefscal.src /energy/energy.src /nbonds/enbfast.src /nbonds/enbond.src /pert/block.src /util/util.src doc/block.doc /dynamc.doc /pdetail.doc .............................................................................. 3.2.2 Distance matrix and radius of gyration restraints New restraint energy terms added to permit restraint of system based on its radius of gyration and/or the value of a reaction coordiante what describes the degree of nativeness based on the number of native side chain contacts. Work due to Felix B. Sheinerman and Erik Boczko. New Keywords RGYCONS and DMCONS. Files added: source/fcm/dmcons.fcm /fcm/rgy.fcm /energy/dmcons.src /energy/rgy.src Files modified: source/charmm/charmm_main.src /charmm/iniall.src /dynamc/dynamc.src /dynamc/dynamcv.src /dynamc/dynamvv.src /energy/energy.src /energy/printe.src /fcm/energy.fcm .............................................................................. 3.2.3 Global-Works-Server (GWS) Port Changes introduced for port to TMC's Global-Works-Server (GWS) which utilzes the Sun UltraSpark machines and Solaris operating system. Files added: build/UNX/Makefile_gws Files modified: install.com source/fcm/impnon.fcm /machdep/machutil.src /machdep/space.src .............................................................................. 3.2.4 Cray T3E Port Port to Cray T3E (Note the clock changes in paral3.src correspond to a 300Mhz T3E clock. For the 450Mhz version this number needs to be changed. The conversion is 3.333e-9 for the 300 MHz version and 2.2222e-9 for the 450 MHz version.) Files added: build/UNX/Makefile_t3e Files modified: install.com source/fcm/heap.fcm /machdep/cstuff.c /machdep/machio.src /machdep/machutil.src /machdep/parallel.src /machdep/parset.src /machdep/space.src /machdep/startup.src, /util/cmdpar.src .............................................................................. 3.2.5 CRAYVEC code modification 1 Modified crayvec source code to accomodate hardwired boundaries (note this also permits interaction energy to work w/ images when bound keyword is specified). Note this changes is tied in with the new EXPAND extensions of B.R. Brooks. Files modified: source/nbonds/cnbnd.src /nbonds/cenbf.src test/c24test/pbound1.inp .............................................................................. 3.2.6 CRAYVEC code modification 2 Added crayvec keyword to nbonds/enbfast.src to permit crayvec option to be compiled and tested on scalar machines. Files modified: source/nbonds/enbfast.src .............................................................................. 3.2.7 ITIME and IDATE Added cspp keyword around itime and idate subroutines to accomodate hpux key being dropped from this place. Files modified: source/machdep/machutil.src .............................................................................. 3.2.8 Environment variable parsing Modified machdep/machio.src to fix logic bug in environment variable parsing for file opens. Files modified: source/machdep/machio.src .............................................................................. 3.2.9 Atom selection Altered selection routines to include periodic bc for selection around point when using pbound pbcs. (FBS addition) Files modified: source/util/selcta.src doc/select.doc Added syntax: SELE POINT real real real CUT real PERIodic END If pbound was not set up, it writes a warning: 'pbound is not set up: PERI is ignored'. .............................................................................. 3.2.10 PBEQ solver Significant overhaul/additions to Poisson-Boltzmann solver. (CLB/MV) Files modified: source/misc/pbeq.src /fcm/pbeq.fcm .............................................................................. 3.2.11 NMR modification Slight modifications to nmr.src. (CLB/MG) Files modified: source/misc/nmr.src .............................................................................. 3.2.12 Lattice reading code Addition of lattice reading code to read Ca and SC coordinates from endpoint of lattice simulations. New keyword LATTICE. (CLB) Files added: source/misc/lattice.src Files modified: source/io/coorio.src .............................................................................. 3.2.13 F90 Compilation (1) Fixed cenerf.src for cray compilations using f90 (undeclared shared variable). (WSY/CLB) Files modified: source/nbonds/cenerf.src (2) Checked compatibility of source w/ f90 compilation on Cray c90. Files added: build/UNX/Makefile_cray_f90 .............................................................................. 3.2.14 Makefile_t3d changed t3d to t3x in Makefile_t3d and machdep/cstuff.c. this is a genereic reference to either cray mpp. (WSY/CLB) Files modified: build/UNX/Makefile_t3d source/machdep/cstuff.c .............................................................................. 3.2.15 Makefile_sgi Introduced changes into Makefile_sgi FC0 option to permit compilation of travel.src. Files modified: build/UNX/Makefile_sgi .............................................................................. 3.2.16 Documentation updates Fix various inconsistencies in doc files and update. Files changed: doc/block.doc /cons.doc /correl.doc /dynamc.doc /energy.doc /nmr.doc doc /pdetail.doc /testcase.doc .............................................................................. 3.2.17 HTML Doc Files - Rick Venable and Charles L. Brooks, III Added html documentation files and developed/modified doc2html.com originally developed at NIH. All relevant files added to support/htmldoc Files added: support/htmldoc/00README /Category_generic.Html /Commands_template.Html /Overview_generic.Html /Charmm_template.Html /MBCO.gif /doc2html.com /p_A-animate.gif ------------------------------------------------------------------------------ 3.3 VIBRAN Enhancement - Herman van Vlijmen In the VIBRAN TRAJ utility normal modes can now be superimposed onto each other. The initial phase of each selected mode can be set to zero or set to random. The keyword STEP (in ps) is mandatory, since the different modes have to be superposed using their respective frequencies. Files modified: source/vibran/vibran.src /vibran/vibio.src doc/vibran.doc test/c20test/vibpafl.inp ------------------------------------------------------------------------------ 3.4 Linux Port Name : Jeffery S. Taylor Email Address : jeff@adeno.wistar.upenn.edu Institution : The Wistar Institute and The University of Pennsylvania Date : November 4, 1996 Proj. Report : B961105.c25 This modification is to make CHARMM compile under the Linux OS with the GNU Fortran compiler, version 0.5.18. There are one or two bug fixes that are unrelated to Linux. For now, all Linux related changes are under the GNU keyword. Files modified: source/machdep/cstuff.c changes to make the date and time functions work. Mostly just changing (float)s to (double)s. source/machdep/machio.src the GNU keyword is added to the appropriate line to make the open file for append command work. source/machdep/machutil.src changes to make time and date functions work. Again, it's mostly changing some variables from REAL to REAL*8. source/machdep/parset.src This is a general bug fix and not Linux related. Newer versions of the PVM message passing libraries have changed and the subroutine PVMFCATCHOUT now requires two arguements. If called with only one the program will hang. source/machdep/startup.src Added code to get the user name for the startup banner. source/misc/testch.src This is a general bug that the finicky GNU compiler complains about. While most compilers don't complain about it, it won't hurt to make it right. Simply, FORMAT(... ,X, ...) must be FORMAT(... ,1X, ...) source/quantum/qmpac.src This is a general bug that the finicky GNU compiler complains about. The original code has a jump into a loop, which some compilers don't like and is generally not good coding practice. source/solvation/fft.src Like the compiler used for the OS/2 version (Watcom?), the GNU compiler requires that complex numbers (x,y) be stated as DCMPLX(x,y). build/UNX/Makefile_gnu change the following: FC = g77 -O2 to FC = g77 -O2 -m486 -fno-strength-reduce -malign-double -ffloat-store FCR = $(FC) -c -O -K -V +R +T -u to FCR = $(FC) -c FCRD = $(FC) -c -g +T +R -V -w to FCRD = $(FC) -c -g The compiler options -m486 and -malign-double increase performance a bit; the -fno-strength-reduce works around a compiler bug and the -ffloat-store is needed to stay out of an infinite loop in 'util/diagq.src'. This last option probably slows thing down and the bad code in 'util/diagq.src' should really be changed. ------------------------------------------------------------------------------ 3.5 Karolinska Institutet Developemnts - Lennart Nilsson 3.5.1 READCV with REWIND In order to be able to reuse READCV without having to open files all the time, all calls to VCLOSE are commented out and a REWIND is added at the beginning. Also added a couple of lines to set variable ?TIME to the current trajectory time when a coordinate set is read. File modified: source/dynamc/dynio.src .............................................................................. 3.5.2 Smart MERGE Make MERGE a little smarter in estimating how many coordinat sets are to be read so STOP does not have to be specified in order to get a viable output file. File modified: source/dynamc/dynsub.src .............................................................................. 3.5.3 ALPHAMP parallel code No need to hardwire program name to charmm for alphamp in parallel startup File modified: source/machdep/parset.src .............................................................................. 3.5.4 DIPOLE Replaced dipole code in corman with call to subroutine DIPOLE which can(will) be used in other places of charmm as well; also documented this option. Files modfied: source/manip/corman.src doc/corman.doc .............................................................................. 3.5.6 SOLANA overhaul Overhaul of SOLANA to resolve parsing/documentation inconsistencies. Use READCV instead of proprietary trajectory reader (here the ability of READCV to re-use files introduced in 3.5.1 is needed). Make trajectory definition according to standard CHARMM usage (NUNIt, FIRSTu,...). Change the various analysis flags into keyword-value pairs with the value being the file unit number onto which results are written. Add simple linear regression to MSD analysis to produce estimate of diffusion coefficient; also set ?DCOEFF to this value (A**2/ps). Files modfied: source/correl/solana.src doc/corman.doc doc/miscom.doc test/c22test/solana.inp .............................................................................. 3.5.7 H-bond analysis COOR HBONd now makes static analysis of current coordinate set if no trajectory specification (no FIRStunit ) is present. Files added: test/c25test/hba1.inp Files modified: source/manip/hbanal.src doc/corman.doc .............................................................................. 3.5.8 TEST COMMunication New command TEST COMM to test parallel communication timings. File modified: source/misc/testch.src .............................................................................. 3.5.9 Bugfixes (1) source/energy/epull.src PULL OFF tried to free unallocated heap space (2) source/charmm/miscom.src FAST OFF did not turn off flag for Charlie's min.image code (3) source/manip/hbanal.src COOR HBONd had an indexing bug which made the lists wrong for some combinations of acceptors&donors when the anggle cutoff was in effect. ------------------------------------------------------------------------------ 3.6 Incorporation of CADPAC6.0 into CHARMM Name : Paul Lyne Email Address : paul@tammy.harvard.edu Institution : Harvard University Date : February 6, 1997 Development of an interface to allow CHARMM to run with CADPAC6.0 when performing QM-MM calculations. CADPAC6.0 can perform HF, MP2, MP3 and DF calculations. The interface is very similar to the GAMESS interface and is found in cadint/cadini.src. Some energy, nbond and update routines were modified to run with CADPAC. A number of multiple declarations are found when compiling "pure" CADPAC with CHARMM and so many of these routines were renamed in CHARMM. Specifically NORMAL ---> NORMALL NORML ----> NORMLL DECOMP ---> DECMP MATINV ---> MATNV SUBVEC ---> SUBVC PROJCT ---> PROJKT ROTAT ----> ROTAIT SQUARE ---> SQUAR TQL2 -----> TQLTWO ONELEC ---> ONELC EXTRA ----> XTRA NATORB ---> NTORB TRED2 ----> TREDTWO HCORE ----> HKORE TQLRAT----> TQLRT SYMTRI----> SYMTREE The files affected by these changes are detailed below. Files Added: source/cadint/cadini.src build/UNX/cadint.mk build/UNX/cadpac.mk Files Modified: Renamed routines MATNV: molvib/molvut.src NORML: mmff/datastruc.src DECMP: misc/pbeq.src NORMLL: dimb/dimbsub.src,dimbutil.src energy/epull.src image/imagio.src manip/corman.src,pucker.src,rotlsq.src misc/nmr.src,zmat.src vibran/raise.src,redbas.src,vibio.src,vibsub.src,vibutil.src util/vector.src TQLTWO: quantum/qmpac.src TQLRT: quantum/qmpac.src NTORB: quantum/qmdata.src,qmset.src,qmene.src,qmset.src fcm/amiparm.fcm SQUAR: quantum/qmjunc.src,qmpac.src SUBVC: manip/pucker.src minmiz/abner.src PROJKT: rxncor/adiab.src,travel.src ROTAT: quantum/qmpac.src XTRA: quantum/qmpac.src,qmene.src,qmjunc.src ONELC: quantum/qmpac.src fcm/am1parm.fcm SYMTREE: fcm/rtf.fcm HKORE: quantum/qmene.src,qmjunc.src TREDTWO: molvib/molvut.src Modified to run with CADPAC: source/charmm/charmm_main.src, iniall.src /energy/energy.src, printe.src /gamint/gamini.src /gener/update.src /nbonds/nbonda.src, nbonds.src /quantum/addlnat.src /fcm/energy.fcm, gamess.fcm install.com New Documentation: doc/cadpac.doc New Testcase: test/c25test/cwat.inp =========================================================================== [4] c25b1 Change Log CHARMM c25a3 (February 15, 1997) to c25b1 (August 15, 1997) 4.1 NIH Developments - Bernard R. Brooks (brbrooks@helix.nih.gov) 4.1.1 Particle Mesh Ewald Code Extension The Particle Mesh Ewald (PME) code has been extended. The following features are now supported: - PERT (free energy calculation) with PME (including pressures) - Assymetric units with CRYSTAL (when NOPEr>0 in CRYStal BUILd command) is now supported with PME. - Total charge (Qtot<>0) energy and pressure correction term has been added. - Accurate pressures for the triclinic (and all other) cases (and for PERT) - Ewald energy components have been separated and can be turned off with the SKIP command ('EWKS','EWSE','EWEX','EWQC','EWUT'). (k-space,self term,exclusion,total Q correction,utility) Some details: - Total system charge is now part of the PSF - PME bug for the SGI fixed (uninitialized stuff) Files Added: source/nbonds/pmeutil.src Files modified: source/energy/energy.src /energy/eutil.src /energy/printe.src /fcm/energy.fcm /fcm/exfunc.fcm /fcm/pert.fcm /fcm/psf.fcm /gener/genpsf.src /gener/modpsf.src /gener/psfsum.src /image/eimage.src /manip/scalar.src /mmff/enbfast_mm.src /nbonds/enbond.src /nbonds/evdwf.src /nbonds/ewaldf.src /nbonds/ewaldf2.src /nbonds/nbonds.src /nbonds/nbutil.src /nbonds/pme.src (major changes) /pert/epert.src /pert/icpert.src /pert/pert.src /pert/tsme.src /util/vector.src .............................................................................. 4.1.2 The crystal facility has been extended The follwing new features have been added: - The "DODE" has been renamed "OCTA" (for truncated OCTAhedron). (pressure bug fixed for OCTA) - A new type "RHDO" has been added (for RHombic DOdecahedron). - The CRYSTAL BUILD command is now much faster and more accurate. The use of the double atom search has been limited. - The documentation has been updated to give detailed information regarding crystal types. - The WRITe/PRINt IMAGE command is no longer iterative (in accord with the existing documentation). Files modified: source/image/crystal.src (major changes) /image/imagio.src .............................................................................. 4.1.3 Overhaul of Harmonic restraints The CONS HARM command has been overhauled and extended. The new syntax has three different types of harmonic restraints: CONStraint HARMonic { [ABSOlute] absolute-specs } force-const-spec { BESTfit coordinate-spec } { RELAtive 2nd-atom-selection } { CLEAr } The ABSOlute is the old method. The BESTfit causes the reference set to be logically bestfit rotated/translated before computing the restraint energy. The RELAtive allows two portions of one PSF to be restrained to the same internal geometry by the bestfit least squares rotation (no reference coordinates used). Some features and changes: - Multiple restraints (same or different types) are allowed. - HARMonic restraint I/O is no longer supported. - The old command syntax still functions (no rewrite of scripts required). - The READ/PRINt/WRITe CONS commands now have a "PSF 0" option for PERT. - PERT supports all of these restraint types. Restriction: - Each atom may participate in AT MOST one harmonic restraint term. Files modified: source/charmm/iniall.src /dynamc/dcntrl.src /energy/ecnstr.src (major changes) /energy/energy.src /energy/intere.src /fcm/cnst.fcm /fcm/dimens.fcm /fcm/euler.fcm /fcm/exfunc.fcm /fcm/pert.fcm /gener/genpsf.src /gener/modpsf.src /gener/replica.src /io/mainio.src /machdep/quanta.src /manip/cstran.src (major changes) /manip/rotlsq.src (major changes) /pert/epert.src /pert/icpert.src /pert/pert.src /quantum/addlnat.src /util/matrix.src .............................................................................. 4.1.4 Enhancement to REPLICA/PATH The REPLICA/PATH method has been extended to allow for bestfit translation and/or rotations between adjacent replicas before computing the restraint energies. Getting the forces right was the hard part. This allows entire molecules to be replicated (or sections with significant freedom). RPATh [ KRMS real ] [ KANGle real ] [ COSMax real ] [MASS] [WEIGht] [ KMAXrms real ] [RMAXrms real ] [ ROTAtions ] [ TRANslations ] Files modified: source/energy/epath.src /energy/ecnstr.src /fcm/rpath.fcm .............................................................................. 4.1.5 AMBER comatibility A "##IF AMBER" keyword has been added. Some of the universal constants have been changed with this keyword to allow for Amber compatibility. For example, CCELEC has been changed from 332.0716 to 332.0522173. Amber topology and parameter files are available (results exactly match Amber). Files modified: source/fcm/consta.fcm /energy/ecntrl.src .............................................................................. 4.1.6 The TRIM command modified The default first and last characters for the TRIM command has been modified to make it easier to strip blanks from parameters. The default is now the first and last non-blank characters. Files modified: source/charmm/miscom.src .............................................................................. 4.1.7 QM/MM update The version of GAMESS has been updated to the March-97 version from Ames lab. Also, QM/MM gaussian blur of MM charges has been implemented as an option. Files modified: source/fcm/gamess.fcm /gamint/gamini.src (major changes) /gamint/gamess/* (all files replaced) /misc/nmr.src .............................................................................. 4.1.8 Bugs and/or Problems Fixed. (1) Image usage and removal of net translation/rotation The selection of which rotational/translational degrees of freedom are invariant to the energy has been fixed (for when Images or Crystal is in use). Files modified: source/dynamc/dcntrl.src /dynamc/prssre.src (2) Reversion of code for CADPAC QM/MM Some minor additions to QM/MM we made to improve the reversion. Lines that were too long were split with continuation lines. Some names were not changed. NATORB <- NATRB ONELEC <- ONELC SUBVEC <- SUBVC HCORE <- HKORE SQUARE <- SQUAR EXTRA <- XTRA ROTAT <- ROTAIT Files modified: source/charmm/iniall.src /energy/energy.src /fcm/am1parm.fcm /gamint/gamini.src /minmiz/abner.src /nbonds/nbonds.src /quantum/addlnat.src /quantum/qmdata.src /quantum/qmene.src /quantum/qmjunc.src /quantum/qmpac.src /quantum/qmset.src (3) Some changes in energy term usage There has been some reorganization of energy term usage. The variables GTOT and CDTOT have been removed (now all QM/MM methods use QMEL). A new output line for Ewald energies has been added. The routine PRINTE and energy.fcm have been modified. Files modified: source/energy/energy.src /energy/eutil.src /energy/printe.src /fcm/energy.fcm (4) Dimension changes MMFF requires larger MAXCT (5500 -> 15500) Files modified: source/fcm/dimens.fcm (5) Changes for parallel CHARMM Missing include file added as a junk file. Parallel calls suppressed when only one node. Bug in parallel READ PARAM APPEND fixed. Extended electrostatics has been made to run in parallel. Some Terra problems fixed Files modified: source/charmm/iniall.src /charmm/miscom.src /energy/energy.src /fcm/shmem.fcm /io/parmio.src /machdep/socket.c /nbonds/exelec.src /nbonds/nbondg.src /nbonds/nbonds.src /pert/epert.src (6) Changes for the LoBoS project The LoBoS project is an attempt at the NIH to creat a high-performance parallel supercomputer from low-cost commodity components (PC type machines) Files modified: source/machdep/socket.c /machdep/startup.src (7) Removal of any embedded double quotes from @param substitution Files modified: source/util/title.src (8) Bug in calling sequence to EBOND fixed with the INTEraction command File modified: source/energy/intere.src (9) Bugs in RESDist code Two unrelated bugs in the resdist code were fixed (one parsing, one in anal). File modified: source/misc/resdist.src (10) Minor bugs in PERT Gets correct long time averages for virial terms. Allows negative lambda increment in AUTO window mode. File modified: source/pert/epert.src /pert/pert.src (11) Function return values set as required in Fortran77 Files modified: source/util/calc.src /util/cmdpar.src (12) Conditional compile problems fixed. Some minor conditional compile problems have been fixed. Files modified: source/nbonds/enbf2.src /nbonds/enbondg.src /nbonds/nbonda.src /pert/epert.src /util/array.src /util/selcta.src /util/vector.src (13) Compile compatibility changes. Some compilers still don't do F77 very well. We made some changes to accomodate these compilers. Also, some changes are needed to better accomodate F90 running in the F77 compatibility mode. Also some C changes for GNU have been made. The use of DCMPLX vs. CMPLX is not standardized across compilers. This requires adding precompile control for this function. Files modified: source/correl/correl.src /correl/corrio.src /image/xtlfrq.src /machdep/cstuff.c /machdep/machutil.src /misc/nmr.src /misc/ssbp.src /nbonds/exelec.src /solvation/fft.src /util/matrix.src (14) Rename of subroutine TRIM The subroutine TRIM has been renamed TRIME (trim end) to provide compatibility with the Absoft compiler. TRIM is a reserved system function/subroutine name for this system. Files modified: source/charmm/charmm_main.src /correl/correl.src /gener/hbonds.src /gener/modpsf.src /graphics/graphx.src /image/images.src /image/imagio.src /io/coorio.src /io/parmio.src /io/univio.src /machdep/machio.src /machdep/parset.src /machdep/startup.src /misc/aspener.src /misc/resdist.src /misc/xray.src /nbonds/nbutil.src /pert/icfix.src /pert/icpert.src /pert/tsmp.src /pert/tsms.src /util/cmdpar.src /util/parse.src /util/selcta.src /util/string.src /util/title.src (15) Printout error in the COOR ORIEnt command fixed. File modified: source/manip/corman.src (16) Clean up of include files and source file endings Some include files and source files were modified to have consistent endings. Files modified: source/fcm/cmdpar.fcm /fcm/control.fcm /fcm/coord.fcm /fcm/deriv.fcm /fcm/distri.fcm /fcm/mscpar.fcm /fcm/ssbp.fcm /fcm/string.fcm /graphics/grutil.src /manip/dynanal.src /util/string.src (17) Comments added Files modified: source/energy/epath.src /fcm/econt.fcm /fcm/bases.fcm /fcm/inbnd.fcm /fcm/mscpar.fcm /fcm/scalar.fcm (18) Unused variables removed Files modified: source/charmm/charmm_main.src /nbonds/ewald.src /pert/block.src /util/calc.src (19) Minor cosmetic changes (some are code reversions). Files modified: source/fcm/contrl.fcm /gener/update.src /io/coorio.src /machdep/space.src /manip/corman2.src /minmiz/conjug.src /misc/noe.src /rxncor/rxndef.src /util/selcta.src ------------------------------------------------------------------------------ 4.2 TSRI Corrections - Charles L. Brooks III (brooks@scripps.edu) (1) MPI related problems are fixed Changes to incorporate mpi libraries on SGI 64 bit platforms are added and MPI related calls are fixed. Files Modified: install.com build/UNX/Makefile_sgi (???) source/machdep/paral1.src (2) T3E parallel code fix get clock speed directly from machine Files Modified: source/machdep/cstuff.c /machdep/paral3.src (3) Update documentation doc/developer.doc : documents for DMCONS, DOCK, LATTICE, LDM, PBOUNDC and RGYCONS doc/parallel.doc : Cray T3E documentation added (4) Add comments source/fcm/dmcons.fcm /rgy.fcm /solana.fcm (5) Uninitialized variables are fixed source/dynamc/mts.src (6) Preprocessor directive fix source/machdep/machutil.src /machdep/socket.c /machdep/startup.src /pert/block.src /pert/epert.src : Declare MTYPE for w/o MMFF =========================================================================== [5] c25b2 Change Log CHARMM c25b1 (August 15, 1997) to c25b2 (February 15, 1998) 5.1 Parallel Code Update - Milan Hodoscek More machines, library, and architectures supported, and some minor fixes: Files modified: source/machdep/cstuff.c (t3e for GAMESS) /machutil.src (for Convex SPP-2000) /parset.src (support for bash,sh added) /paral1.src /paral2.src /paral3.src /socket.c (for HP - sometimes vfork doesn't work) ------------------------------------------------------------------------------ 5.2 Bugfixes (1) tool/prefx.f Unused variables removed: J. JPT, LBLANK, LPAREN (2) source/minmiz/tndriv.src - Milan Hodoscek DATA statement placed after declarations (3) source/solvation/fft.src /util/imsl.src - Milan Hodoscek Non-standard F77 calls fixed: DREAL is replaced by DBLE (4) source/mmff/merckio.src - Milan Hodoscek There is a call to TIME routine which is not machine independent. It is replaced with the write statement, since above it there is a call to machine independent routine. (5) source/energy/intere.src - Bernard R. Brooks (B970918.rp and B970920.brb) Fix atom selection logic and QCOMP parsing (6) source/image/nbondm.src - Bernard R. Brooks (B970920.brb) remove unused NGAT and initialize NREM (7) source/vibran/vibio.src - Bernard R. Brooks (B970920.brb) initialize ICNTRL (8) source/image/xtlfrq.src - Bernard R. Brooks (B970920.brb) zero ICNTRL (9) source/io/coorio.src - Bernard R. Brooks (B970920.brb) DIM4 CRD I/O fix (10) source/io/psfres.src - Bernard R. Brooks (B970920.brb) Error message corrected (11) source/nbonds/cenbf.src - Charles L. Brooks, III (B980106.clb) Fix bad coding (12) source/nbonds/enbfast.src - William S. Young (B980106.clb and B980106.brb) Declear TFELEC and TFVDW (13) source/mmff/efast_mm.src /enbscalar_mm.src - Charles L. Brooks, III (B980106.clb) uninitialized variables fixed (14) source/graphics/iris_graphics.c - Charles L. Brooks, III (B980106.clb) #ifndef nographics - #endif added (15) soruce/correl/solana.src - Dan Strahs (B971011.ds) I/O unit handling fixed (16) source/io/parmio.src - Emanuele Paci (B980112.ep) NBFIXN counter increment moved out of ADDNBF (17) source/gener/modpsf.src - Youngdo Won In JONSG, set ?NSEG by the PSFSUM call at the end