--------------------------------------------------------------------------- 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 CHARMM 26.0 c26a1 Developmental August 15, 1997 c26a2 Developmental February 15, 1998 c26b1 Release September 30, 1998 c26b2 Release February 15, 1999 CHARMM 27.0 c27a1 Developmental September 30, 1998 c27a2 Developmental February 15, 1999 c27b1 Release August 15, 1999 c27b2 Release February 15, 2000 c27b3 Release August 15, 2000 c27b4 Release February 15, 2001 CHARMM 28.0 c28a1 Developmental August 15, 1999 c28a2 Developmental February 15, 2000 c28a3 Developmental August 15, 2000 c28a4 Developmental February 15, 2001 c28b1 Release August 15, 2001 c28b2 Release February 15, 2002 CHARMM 29.0 c29a1 Developmental August 15, 2001 c29a2 Developmental April 15, 2002 c29b1 Release August 15, 2002 c29b2 Release February 15, 2003 CHARMM 30.0 c30a1 Developmental August 15, 2002 c30a2 Developmental February 15, 2003 c30a2x Evaluation February 15, 2003 c30b1 Release August 15, 2003 c30b2 Release February 15, 2004 CHARMM 31.0 c31a1 Developmental August 15, 2003 c31a2 Developmental February 15, 2004 c31b1 Release August 15, 2004 c31b2 Release February 15, 2005 CHARMM 32.0 c32a1 Developmental August 15, 2004 c32a2 Developmental February 15, 2005 c32b1 Release August 15, 2005 c32b2 Release February 15, 2006 --------------------------------------------------------------------------- [0] About CHARMM32 Development At the July 2004 CHARMM meeting (Harvard University, July 9-10, 2004), we decided to release CHARMM c31b1 with incorporating enhancements and fixes to the developmental version c31a2. The modified source code and features are described in ChangeLog.c31, [4] c31b1 Change Log. As an on-going project, CHARMM development will be carried out with CHARMM version 32a series. The following describes new features and enhancements incorporated in the c32 development period. =========================================================================== [1] c32a1 Change Log The following are introduced and modified during the development period of February 15, 2004 through August 15, 2004. The developments are based on CHARMM version c31a2. Some enhancements and fixes to c31a2 are also incorporated into c31b1 as described in the c31b1 release note (ChangeLog.c31). 1.1 University of Wisconsin Developments Developers : Patti Schaefer, Mark Formaneck and Qiang Cui Email Address : cui@chem.wisc.edu, psschaefer@wiscmail.wisc.edu formanec@chem.wisc.edu Institution : University of Wisconsin, Madison Date : July 1, 2004 1.1.1 GSBP and eWald Sum Codes added to the SCC-DFTB/MM Framework The generalized solvent boundary potential (GSBP) originally developed by Roux and co-workers for MM simulations, has been combined with the SCC-DFTB/MM code. In addition, eWald summation has been integrated with SCC-DFTB/MM. These developments can be extended in straightforward manners to other QM codes, although the implementation is somewhat easier for SCC-DFTB due to its specific representation of charge density. Files Added: source/fcm/sccgsbp.fcm source/misc/gsbpscc.src source/sccdftbint/sccdftbsrc/ktable_ewscc.f (Setting up kspace table) source/sccdftbint/sccdftbsrc/long_sccmm1.f (Different ways of getting source/sccdftbint/sccdftbsrc/long_sccmm2.f the eWald potential) Files Removed: source/sccdftbint/sccdftbsrc/xnorm.f source/sccdftbint/sccdftbsrc/vnorm.f Files Modified: build/UNX/sccdftb.mk (removed xnorm,vnorm; added long_sccmm1/2; ktab*) source/energy/energy.src (GSBP/Mulliken) source/fcm/sccdftb.fcm (added Mulliken, ewald) source/fcm/blockscc.fcm (Cleaned up) source/fcm/pbeq.fcm (GSBP exclusion for QM/MM) source/misc/gsbp.src (GSBP) source/misc/pbeq.src (related to GSBP) source/nbonds/nbonds.src (remove warning about eWald) source/sccdftbint/sccdftbsrc/dylcao.f (ewald) source/sccdftbint/sccdftbsrc/eglcao.f (GSBP) source/sccdftbint/sccdftbsrc/external*f (ewald) source/sccdftbint/sccdftbsrc/gamma.f (charge-Hubbard) source/sccdftbint/sccdftbsrc/gammamat.f (ewald) source/sccdftbint/sccdftbsrc/long_range.f (ewald) source/sccdftbint/sccdftbsrc/mulliken.f (added Mulliken transfer) source/sccdftbint/sccdftbsrc/shift.f (GSBP and charge-Hubbard) source/sccdftbint/sccdftbini.src (ewald/Mulliken/Hubbard enforce FAST OFF for DTSC-FEP) Modified Documentation: sccdftb.doc New Testcases: c32test/scc_fep_dtsc.inp (DTSC-FEP calculations for redox potential) data/top_qc27.inp data/par_qc27.inp (include FAD) data/chox_sb_scal_q.psf data/chox_minimized.crd data/chox_sb_q.cns data/chox_sb_q-min.crd data/chox_st_equ_one.res c32test/scc_pka1.inp c32test/scc_pka2.inp (DTSC-FEP pKa calculations for EtSH) data/etsh.psf,etsh-min.crd data/etsh-pka1-equ-0.70.res data/etsh-pka2-equ-0.95.res c32test/scc_ewald_triala.inp (eWald calculation with SCC-DFTB/MM for solvated tri-alanine) data/triala_solv.psf data/triala_solv.crd c32test/sccgsbp1_2cba.inp (examples for setting up an enzyme c32test/sccgsbp2_2cba.inp - carbonic anhydrase - calculation c32test/sccgsbp3_2cba.inp using SCC-GSBP) c32test/sccgsbp4_2cba.inp data/top_ca.inp (included Zinc related RTF) data/par_ca.inp data/2cba.psf (solvated carbonic anhydrase) data/2cba.crd Note: making sccdftb.a automatically added to the Makefile by install.com requires adding "sccdfbint.a" into the default object list in build/UNX/Makefile* .............................................................................. 1.1.2 BNM and DTSC Codes Cleaned Codes for block normal mode analysis (BNM) and the dual-topology- single-coordinate(DTSC) SCC-DFTB/MM FEP calculations (including pKa) have been cleaned up. Files Modified: source/vibran/vibran.src (adopted patch) source/energy/eintern.src (adopted VIBRAN---> VIBPARA; fix for DTSC-FEP) source/energy/energy.src source/dynamc/dcntrl.src (fix for DTSC-FEP) source/dynamc/dynamc.src source/dynamc/dynamc4.src source/dynamc/dynamcv.src source/dynamc/dynamvv.src source/dynamc/dynio.src source/misc/eef1.src (adopted VIBRAN---> VIBPARA) source/nbonds/enbond.src source/nbonds/nbonda.src source/nbonds/nbondg.src source/nbonds/nbonds.src source/nbonds/enbonda.src (fix for DTSC-FEP) Modified Documentation: vibran.doc Modified Testcase: bnmtest.inp (modified BNM input) .............................................................................. 1.1.3 New CONS RMSD Functional Form Added the Zeta functional form to the Relative RMSD restraint. Also added two atoms selection - atoms in first selection are affected by the restraint, atoms in the second selection are used in fitting the reference structures. In order to utilize these two selections, the fitting and restraint application routines were separated (before, this was done in the same routine) and the arrays were reworked. This will cause some extra work for using the code in the manner that was originally coded for, but the results are the same. Also, we added functionality to call the fitting routine every INRT steps, which can help to save on calculation time. Files Modified: source/energy/ecnstr.src (addition of extra HEAP space, used in ECNST3) source/energy/rmsd.src (Major Changes, Added Subroutines) source/fcm/rmsd.fcm (added variables) source/manip/cstran.src (added selection array, KSLCT, used in SETRMSD0) Modified Documentation: doc/cons.doc New Testcase: c32test/cons_rmsd_zeta.inp data/cons_rmsd_zeta.psf data/cons_rmsd_zeta-ref1.crd data/cons_rmsd_zeta-ref2.crd .............................................................................. 1.1.4 New TMD Functional Form Added capability to use two different target structures with TMD, using the Zeta form of the constraint only. Now, two selections can be used for either form (original or new) of the TMD constraint - first selection is for fitting targets, second selection is for applying the TMD constraint. One selection defines both functionalities for the same selection. Most of the code for the original, one-target TMD has been untouched, and extra subroutines were created for the Zeta form. Also, added a call to fit the targets to the current structure upon calling dynamics, instead of waiting until step=INRT, as first implemented. This new code is not parallelized. Files Modified: source/dynamc/dcntrl.src (Major Changes, added Zeta terms) source/dynamc/dynamc4.src (minor 'call wridyn' changes) source/dynamc/dynamc.src (Major Changes, added Zeta terms) source/dynamc/dynio (readyn and wridyn uses more variables for Zeta form, and a second target structure is saved in restart file) source/dynamc/tmd.src (Major Changes, Added Subroutines) source/fcm/tmd.fcm (added variables) source/io/coorio.src (minor 'call readyn' changes) source/io/mainio.src (now can read and write 2nd target structure) source/mbond/mbback.src (minor 'call wridyn' changes) source/mc/mcio.src (minor 'call readyn/wridyn' changes) source/mc/mvhmc.src (minor 'call dynamc' changes) Modified Documentation: doc/dynamc.doc New Testcase: c32test/tmd_zeta.inp ------------------------------------------------------------------------------ 1.2 TSRI Developments Developers : Scott Brozell, Mike Crowley, Charles L. Brooks, III Roberto GOmpers (SGI) Email Address : sbrozell@scripps.edu, crowley@sripps.edu, brooks@scripps.edu Institution : The Scripps Research Institute Date : July 4, 2004 1.2.1 4-Byte Integer Binary IO 64 bit integers are default for many architectures now. Trajectories and other binary files written by charmm are unreadable on other machines when the binary files contain 64 bit integers. This mod makes all binary io restricted to 32 bit integers only Files Modified: install.com source/correl/solana.src /dimb/dimbsub.src /dynamc/dynio.src /dynsub.src /fcm/iochan.fcm /deflts.fcm /gener/hbonds.src /image/xtlfrq.src /io/coorio.src /parmio.src /psfres.src /machdep/cstuff.c /machio.src /manip/corman2.src /intcor.src /molvib/molvio.src /nbonds/etable.src /util/datstr.src /title.src /util.src /vibran/rbquas.src /redbas.src vibio.src Modified Testcase: c31test/endian.inp .............................................................................. 1.2.2 Performance Enhancement of ENBFS8 Loop rearrangement and temporary arrays for locality to speed up fast nonbond routine. Files Added: source/fcm/enbfs8p.fcm source/nbonds/enbfs8p.src Files Modified: install.com source/nbonds/enbfast.src /util/new_timer.src .............................................................................. 1.2.3 64 bit Parallel and Serial IBMAIX Codes (Mike, Could you put a few words here?) Files Added: build/UNX/Makefile_ibmaix /Makefile_ibmaix64 /Makefile_ibmaixmp64 Files Modified: install.com source/correl/solana.src /machdep/cstuff.c /paral1.src /paral2.src /space.src /manip/shake.src /nbonds/pmeutil.src ------------------------------------------------------------------------------ 1.3 Developments at the National Institute of Health Developers : H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks Email Address : hlwood@nih.gov, wuxw@nhlbi.nih.gov, brb@nih.gov Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH Date : July 1, 2004 1.3.1 New Monte Carlo-minimization/annealing (MCMA) method A Monte Carlo-minimization/annealing (MCMA) routines for biased sampling of polypeptide conformations and for docking simulations has been added. This method is based on the IC tables in CHARMM and been demonstrated to work very well in determining low energy conformation of proteins. 1. Moves for peptide/protein structure prediction: bias, back, main, side, all 2. Moves for docking one molecule (segid SEGMOV, resid RESMOV): rota, tran, rotr Acceptance of docking moves: accm, accr, acct, accb or rotated (or both) each step. Random changes are made to PHI, PSI, COS(THETA) and X, Y, Z. PHI, PSI, and THETA are the Euler angles specifying the current orientation of the ligand relative to the previously accepted orientation. References: PJ Steinbach, Proteins 2004, in press. Abagyan & Totrov, JMB 1994. Li and Scheraga, PNAS 1987. Files Added: source/fcm/mcma.fcm source/mc/mcma.src File Modified: source/charmm/charmm_main.src .............................................................................. 1.3.2 Autogenerate for Patching Option An autogenerate feature has been added to the RTF reader and the PATCh command which allow the autogeneration of angles and dihedrals. The PATCH command syntax: PATCh misc-patch-spec residue-list-spec misc-patch-spec ::= [SORT] [SETUp] [WARN] [ ANGLe ] [ DIHEdrals ] [ NOANgle ] [ NODIhedral] The RTF reader AUTOgenerate command syntax: AUTOgenerate [ ANGLes ] [ DIHEdrals ] [ PATChes ] [ NONE ] [NOANgles] [NODIhedrals] [NOPAtches] Note that autogenerate is not the default and must be requested. The specifications in the PATCH command override the specification in the RTF. Files Modified: source/charmm/iniall.src source/fcm/rtf.fcm source/gener/genpsf.src source/gener/modpsf.src source/io/rtfio.src .............................................................................. 1.3.3 New MANTIM STATe and HEAViside Functions CORRECL has two new operations, STATe and HEAViside. MANTIME name { STATe minv maxv } ! Q(t) = 1 (minv < Q(t) < maxv), else = 0 { HEAViside } ! Q(t) = 0 (when Q(t)<0), else = 1 Files Modified: source/correl/correl.src source/correl/mantim.src .............................................................................. 1.3.4 New Crystal type "RECTangular" A new crystal type "RECTangle" has been added to the CRYStal DEFIne command. This new type is the same as "ORTHorhombic", except that the ratios of the unit cell dimensions are fixed. The total volume may change. RECTangular - a/A = b/B = c/C and alpha = beta = gamma = 90.0 degrees. (Note: A,B,C are the initial a,b,c values) (example: 50.0 40.0 30.0 90.0 90.0 90.0 ) (volume = c*b*a) (degrees of freedom = 1) The undocumented ISOTropic option in the DYNAmics command has been removed, since it never worked properly and the new code make its intended function obsolete. Files Modified: source/dynamc/dynamvv2.src source/dynamc/prssre.src source/energy/energy.src source/fcm/image.fcm source/image/crystal.src source/image/eimage.src source/image/xtlfrq.src source/mc/mcener.src source/mc/mcmini.src source/minmiz/abner.src source/minmiz/conjug.src source/minmiz/egrad1.src source/minmiz/nraph.src source/minmiz/powell.src source/minmiz/steepd.src source/minmiz/tndriv.src source/misc/testch.src source/pert/epert.src .............................................................................. 1.3.5 Isotrop Periodic Sum Code (IPS) A new isotropic periodic sum method has been developed. This code is intended as a reasonable alternative to Ewald and vdw LRC correction methods. The new code has been developed for 3-D, 2-D and 1-D periodic systems. There are lots of new options, but the main nonbond keywords are [EIPS] [VIPS] [RIPS real]. See nbonds.doc for details. Files Added: source/fcm/nbips.fcm source/nbonds/enbips.src test/c31test/ips_tip216.inp Files Modified: doc/nbonds.doc source/energy/energy.src source/fcm/inbnd.fcm source/image/nbondm.src source/nbonds/enbfast.src source/nbonds/enbond.src source/nbonds/enbonda.src source/nbonds/enbondg.src source/nbonds/nbonda.src source/nbonds/nbondg.src source/nbonds/nbonds.src source/nbonds/nbutil.src .............................................................................. 1.3.6 Add SCALAR WRITE Command There is a new SCALar WRITe command to output data arrays in CHARMM. File Modified: source/manip/scalar.src .............................................................................. 1.3.7 New Expanded Fast Routines and Fast Control A new set of FAST routines have been developed. These have been written as a single routine that becomes expanded into many "cleaned" routines that are free of unnecessary code (e.g. IF tests). Use of these routines will significantly improve performance. FAST OFF ! Use the slow full-feature routines FAST GENEric ! Use the old "fast" routines (that are no longer fast) FAST ON ! Use best routine available for current calculation FAST EXPAnd ! Use new expanded routines Files Added: source/nbonds/enbaexp.src source/nbonds/enbgexp.src Files Modified: source/charmm/miscom.src source/energy/enefscal.src source/energy/energy.src source/energy/intere.src source/fcm/fast.fcm source/image/eimage.src source/mbond/mbdiag.src source/mc/mcimge.src source/misc/genetic.src source/nbonds/enbond.src source/pert/epert.src source/pert/icfcnf.src source/pert/icpert.src source/pert/tsme.src source/vibran/vibblock.src .............................................................................. 1.3.8 Inline ERFC Code for Faster Ewald The ERFC lookup table code has been simplified (fewer operations) and now works with a zero distance (good for DRUDE), which eliminated a pair of inner loop IF tests. Files Modified: source/cff/ewald_cff.src source/fcm/ewald.fcm source/mmff/enbscalar_mm.src source/nbonds/ewald.src source/nbonds/nbutil.src .............................................................................. 1.3.9 Improve the PRESsure INSTantaneous Command. The PRESsure INSTantaneous command now works with a zero temperature. Additional virial and pressure data is printed. Files Modified: source/dynamc/prssre.src .............................................................................. 1.3.10 NUMLP Set ?NUMLP variable for the number of lonepairs. Files Modified: source/dynamc/lonepair.src source/gener/psfsum.src .............................................................................. 1.3.11 PRNLEV Control Change PRNLEV values to improve print control. Files Modified: source/energy/printe.src source/image/images.src source/nbonds/heurist.src source/nbonds/nbonds.src .............................................................................. 1.3.12 Energy Call Control To facilitate routine selection in ENBOND, a universal flag, QGCMC, has been added. (Aaron, would you check on this? mctest02.inp seems to generate energy blow-out. I fixed part of it, yet does not work correct.) Files Modified: source/charmm/iniall.src source/fcm/gcmc.fcm .............................................................................. 1.3.13 Move ACE Code The ACE common block code was added to a structured data file in fcm/inbnd.fcm (which violates the rules governing structured data files). It also inhibited further development of inbnd.fcm. The ACE arrays have been moved to the file fcm/ace.fcm. File Added: source/fcm/ace.fcm Files Modified: source/charmm/iniall.src source/dynamc/dcntrl.src source/fcm/inbnd.fcm source/io/mainio.src source/manip/cstran.src source/manip/scalar.src source/mc/mc.src source/mc/mcace.src source/mc/mcener.src source/nbonds/ace.src source/nbonds/nbonds.src source/nbonds/nbutil.src source/util/selcta.src .............................................................................. 1.3.14 Set KBT and expand format statement The variable KBT was not properly set. File Modified: source/dynamc/dcntrl.src .............................................................................. 1.3.15 Optional Exit for SHAKE Error Added an optional exit for SHAKE tolerance exceeded errors. By setting BOMLEV to 1 or more, you can make CHARMM die on this error. File Modified: source/manip/shake.src .............................................................................. 1.3.16 Fix bugs/problems with ##IF usage There were a number of ##IF control problems. The use of the inline precompile selection: !##IF CHEQ is wrong. The correct syntax is !##CHEQ Also, spaces within ## line identifiers is not allowed. Files Modified: source/fcm/param.fcm source/fcm/traj.fcm source/fcm/vibblock.fcm source/image/upimag.src source/vibran/vibran.src .............................................................................. 1.3.17 Fix QECONT and ATOMON Bugs The use of QECONT and filling the ECONT array was wrong. File Modified: source/misc/eef1.src .............................................................................. 1.3.18 Fix SCALAR READ Parallel Bug There was a bug in the SCALar READ command when used in a parallel calculation. This has been fixed. File Modified: source/manip/scalar.src .............................................................................. 1.3.19 Fix Compile and Timer Bugs in SPAS Code The SPAS code would not compile properly. It still does not work and it consumes massive quantities of memory... The code should be reworked or removed. Files Modified: source/energy/energy.src source/io/parmio.src .............................................................................. 1.3.20 NUMBERs and CONSTANTs The use of real*8 numbers in calling sequences has been corrected. This is non-standard and causes problems on some compilers. Also, I made an effort to make the use of constants more consistent. For example, I replaced instances of 332.0... with the parameter CCELEC in fcm/consta.fcm. Files Modified: source/dynamc/dynamcv.src source/dynamc/dynamln.src source/dynamc/dynamvv.src source/dynamc/dynamvv2.src source/energy/ecmap.src source/energy/gbmv.src source/energy/gbsw.src source/fcm/consta.fcm source/io/coorio.src source/io/rtfio.src source/mbond/mbback.src source/mc/mcio.src source/misc/genetic2.src source/nbonds/pmeutil.src source/util/random.src .............................................................................. 1.3.21 Fix Spelling File Modified: source/fcm/rndnum.fcm .............................................................................. 1.3.22 QM/MM Interface Using the Q-Chem Quantum Chemistry Package Added a QM/MM interface to Q-Chem using the GAMESS-US and GAMESS-UK interface as a model. Q-Chem and CHARMM communicate via files rather than common blocks which means the two programs live separately. The Q-Chem QM/MM interface was also extended to function with the highly parallel Replica/Path and the Nudged Elastic Band Methods. Files Modified: install.com source/charmm/charmm_main.src source/charmm/iniall.src source/energy/energy.src source/fcm/gamess.fcm source/fcm/replica.fcm source/fcm/path.fcm source/gener/update.src source/gukint/gukini.src source/nbonds/nbonda.src source/nbonds/nbonds.src source/quantum/addlnat.src .............................................................................. 1.3.23 Q-Chem Input Generation Added the ability of zmat.src to write out Q-Chem input files. This occurs in the same way that the Gausssian interface is used. File Modified: source/misc/zmat.src .............................................................................. 1.3.24 Off-Path Optimization and Simulation The new EPATHO procedure was added which allows a user to run orthogonal simulations at each replica/bead/point along a replica or NEB path. These simulations are used to compute the free energy of reaction. Curvature corrections to these simulations were also added, but have not been throughly tested to determine their usefulness. Files Modified: source/energy/epath.src source/fcm/path.fcm source/fcm/replica.fcm source/fcm/gamess.fcm ------------------------------------------------------------------------------ 1.4 Developments at NIC-Slovenia Names : Milan Hodoscek Email Address : milan@cmm.ki.si Institution : National Institutes of Chemistry, Ljubljana, Slovenia Date : June 30, 2004 1.4.1 New version of GAMESS supported New version of GAMESS (19 May 2004 (R3)) is interfaced with CHARMM. New features include Fragment MO, NMR shifts, improved DFT convergence and many others. Files Modified: doc/gamess.doc source/fcm/gamess.fcm source/flucq/fluqqmmm.src source/gamint/blur.src source/gamint/ddi.src source/gukint/gukini.src source/gamint/gamess/{grd2a.src,int1.src,mccas.src,prplib.src, prppop.src,prpel.src,unport.src,zunix.c, gamess.src,grd1.src,guess.src,inputb.src, inputc.src,iolib.src,scflib.src,rhfuhf.src, inputa.src} .............................................................................. 1.4.2 Parallelization of DRUDE, LONEPAIR and VV2 integrator DRUDE and VV2 integrator are parallelized. For efficiency also LONEPAIR had to be parallelized. Files Modified: source/gener/drude.src source/manip/holonom.src source/machdep/paral1.src source/energy/ediff.src source/energy/energy.src source/dynamc/lonepair.src source/dynamc/dcntrl.src source/dynamc/dynamvv2.src source/dynamc/dynamcv.src source/dynamc/dynamc.src source/dynamc/dynio.src source/nbonds/nbonds.src .............................................................................. 1.4.3 Parallelization of SSBP and GSBP Spherical Solvent Boundary Potential method was parallelized. General Solvent Boundary Potential method parallelization started. Currently works in parallel environment, but not parallelized yet. Files Modified: doc/parallel.doc source/energy/energy.src source/misc/ssbp.src source/misc/gsbp.src source/misc/pbeq2.src .............................................................................. 1.4.4 Enhancements for GRAPE interface Several enhancement in the GRAPE interface. Files Modified: source/nbonds/grape.src .............................................................................. 1.4.5 Fix and extension of SOLANA The calculation of rotational correlation in SOLANA was wrong. It is fixed and extended to use Legendre polynomials of second order, by introducing new command keyword RLP . Files Modified: doc/corman.doc source/charmm/iniall.src source/correl/solana.src source/fcm/corman.fcm .............................................................................. 1.4.6 Parallelization of RANDOM code and fix for NEWRNG Parallelization of standard RANDOM number generator. Also the usage of CLCG generator was fixed at the same time. Files Modified: source/charmm/iniall.src source/correl/solana.src source/dynamc/dcntrl.src source/dynamc/dynamc.src source/energy/gbmv.src source/fcm/clcg.fcm source/fcm/parallel.fcm source/manip/intcor.src source/mc/mc.src source/misc/genetic.src source/misc/pbeq.src source/util/clcg.src source/util/random.src source/vibran/vibran.src .............................................................................. 1.4.7 Fixes for various ## keywords Some of the ## keywords would not allow compilation of CHARMM if excluded from pref.dat. New set of fixes for this are in: Files Modified: source/energy/eintern.src source/energy/energy.src source/nbonds/enbfast.src source/nbonds/nbonds.src source/mc/mcener.src ------------------------------------------------------------------------------ 1.5 Harvard Developments Name : Arjan van der Vaart, Robert Petrella Email Address : arjan@tammy.harvard.edu, petrella@tammy.harvard.edu Institution : Harvard University Date : June 29, 2004 1.5.1 Revision of TMD. Enhancement and streamlining of the TMD code. Introduced the "FRMS" keyword, that causes TMD dynamics to stop when a user defined rmsd has been reached. Introduced a selection statement for TMD, that allows application of TMD to a subset of atoms. Removed all TMD statements in the DYNA command: all TMD commands are now parsed in the TMDInitialize command. Removed the NTAR and TARGET keywords since these are redundant. Removed writing of TMD info to restart files, and TMD memory is now deallocated upon finish of DYNA command. Files Modified: source/charmm/charmm_main.src source/dynamc/dcntrl.src source/dynamc/dynamc4.src source/dynamc/dynamc.src source/dynamc/dynio.src source/dynamc/tmd.src source/energy/eutil.src source/fcm/tmd.fcm source/io/coorio.src source/io/mainio.src source/mbond/mbback.src source/mc/mcio.src source/mc/mvhmc.src source/minmiz/minmiz.src New Documentation: doc/tmd.doc Modified Documentation: doc/dynamc.doc doc/io.doc Modified Testcase: test/c31test/tmdtest32.inp .............................................................................. 1.5.2 BYCC Enhancements (Bob, would you like to review this section and edit into a "uniform" format?) 1) SUBROUTINE NBNDCC made into two routines: NBNDCCF --for fastest execution, stripped of options NBNDCCO --for compatibility with various options. The latter routine is the one where developers should add functionality to BYCC. 2) BYCC made compatible with heuristic updates (for both atom-based and group-based calculations) 3) Changes in logic for calling cluster-generating routine (SUBROUTINE CLSBYRULE). A) Clusters are made by default prior to updating the list if "BYCC" is specified in the update command (unless they have previously been made). B) An informed guess is made as to whether the connectivity or the topology of the system has changed before calling NBNDCC. If a change is detected, the clusters are remade prior to non-bonded list generation. This is done because changes in the connectivity may necessitate the formation of new clusters, and significant changes in the topology almost certainly do. (changed subroutine: GTNBCT) 4) added global bycc QLBYCC in actclus.fcm to indicate BYCC has been specified in non-bonded command (for use in other parts of charmm). 5) minor modifications in eef1 code for compatibility with BYCC 6) BYCC made compatible with TSM 7) clustering algorithm made faster (now clusters roughly 1,000,000 atoms/s on 2.66 GHz Pentium 4) Files Modified: source/charmm/iniall.src source/nbonds/nbndcc.src source/nbonds/nbonds.src source/nbonds/nbutil.src source/misc/eef1.src source/fcm/actclus.fcm ------------------------------------------------------------------------------ 1.6 Developments at University of Vienna Developers : Tibor Rudas, Stefan Boresch and Othmar Steinhauser Email Address : tibi@mdy.univie.ac.at and stefan@mdy.univie.ac.at Institution : Molecular Dynamics and Biomolecular Simulation group at the Department of Theoretical Chemistry and Molecular Structural Biology, University of Vienna Date : June 23, 2004 1.6.1 COM Centering in COOR DIPO When calculating the dipole moment of a set of atoms carrying a total net charge the coordinates of this set are recentered to the center of geometry of these atoms. Adding a MASS keyword to the invocation (which is present for many other COOR commands) allows the center of mass as locus of recentering. Both this keyword and the recently introduced OXYZ keyword (which avoids this recentering unsing the absolute coordinates) are also introduced into the DIPO series of CORREL. All calls to CDIPOLE are updated but where no use/parsing of a MASS keyword is provided/necessary .FALSE. and 0 are passed instead of MASS and AMASS (solana.src) Files Modified: source/correl/correl.src source/correl/anacor.src source/correl/solana.src source/manip/corman.src Modified Documentation: doc/corman.doc doc/correl.doc .............................................................................. 1.6.2 SHELLs of Different Thickness Instead of the (still supported) keyword SHTH which defines a single thickness used for all shells generated shells of different thickness can be defined by using the new SHBO keyword. Following this keyword should be NSHL real numbers which represent the boundaries between the single shells (so these numbers should all be in increasing order). Files Modified: source/fcm/shell.fcm source/correl/shell.src source/charmm/iniall.src Modified Documentation: doc/shell.doc Modified Testcase: test/c31testshell.inp ------------------------------------------------------------------------------ 1.7 Karolinska Institute Fixes and Enhancements Developer : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : July 1, 2004 1) Added possibility to compute water-dipole rotational correlation fcn (P1 or P2), also works in shell defined by RSPIN & RSPOUT Files Modified: source/correl/solana.src doc/corman.doc test/c27test/solanal2.doc (seemed unnecessary to add another file for this) 2) Set CHARMM variable CFNORM to the normalization used in CORREL CORFUN, and added possibility to supply the normalization value to be used by CORFUN; useful to get correctly normalized partial correlation fcns. Files Modified: source/correl/solana.src source/correl/correl.src source/correl/corfun.src doc/correl.doc doc/subst.doc 3) Added substitution variables CPUTIME and ELATIME Files Modified: source/machdep/machutil.src doc/subst.doc 4) Corrected documentation of defaults for CORREL CORR (Legendre pol. P0 is a constant..) File Modified: doc/correl.doc ------------------------------------------------------------------------------ 1.8 Implicit Membrane Model 1 (IMM1) and EEF1 update Developer : Themis Lazaridis Email Address : tlazaridis@ccny.cuny.edu Institution : City College of New York/CUNY Date : May 17, 2004 IMM1 is an extension of the EEF1 implicit solvation model to lipid membranes. The membrane hydrocarbon interior is modeled as cyclohexane, with a smooth, monotonic transition between the interior and the aqueous region. Electrostatic screening is modeled using a modified distance-dependent dielectric function (eps=r**l, where l depends on the position of the two atoms with respect to the membrane. In addition, updated parameters for EEF1 are provided (referred to as EEF1.1) and also a version of EEF1 based on CHARMM22. Files Added: support/aspara/toph19_eef1.1.inp support/aspara/param19_eef1.1.inp support/aspara/top_all22_prot_eef1.inp support/aspara/top_all22_prot_eef1.1.inp support/aspara/solvpar22.inp Files Modified: source/fcm/eef1.fcm source/energy/energy.src source/energy/intere.src source/misc/eef1.src source/nbonds/enbfast.src support/aspara/solvpar.inp Modified Documentation: doc/eef1.doc ------------------------------------------------------------------------------ 1.9 Multiple Gaussian Job Input Generation Developers : Victor Anisimov and Alex D. MacKerell, Jr. Email Address : victor@outerbanks.umaryland.edu Institution : University of Maryland Date : June 28, 2004 Gaussian program uses "--link1--" string to separate multiple jobs. On the other hand hyphen symbol is treated by CHARMM as line continuation instruction. As a result, CHARMM was merging the "--link1--" string, which is a Gaussian instruction, with the next line. A correction has been made to instruct the CHARMM command line reader to turn off the line continuation mechanism for the moment of Gaussian file generation. The command line parser ignores hyphen symbol when the parser is invoked from G94INP routine. Logical variable USEHYP is introduced for this purpose. USEHYP set to .TRUE. enables line continuation mechanism (CHARMM default). USEHYP set to .FALSE. disables line continuation (call from G94INP routine). File Modified: source/util/parse.src ------------------------------------------------------------------------------ 1.10 Grand Canonical Monte Carlo Enhancements Developers : Aaron R. Dinner, Hyung-June Woo and Benoit Roux Email Address : dinner@uchicago.edu Institution : The University of Chicago Date : July 19, 2004 The grand canonical Monte Carlo (GCMC) code was substantially enhanced, essentially completing its implementation for molecular liquids like water in the presence of protein solutes. In particular, the following was done: 1. Orientation bias for insertion was added. 2. The grid update is now exact, rather than approximate, allowing grand canonical simulations involving the movement of arbitrarily large rigid bodies (e.g., protein side chains). Memory usage was also improved. 3. Support for the GSBP energy term was added. However, the full term is calculated at each MC step, making it computationally costly. 4. Various minor deficiencies in the initial implementation were corrected. Files Modified: doc/mc.doc source/mc/mc.src source/mc/mcener.src source/mc/mcio.src source/mc/mvgcmc.src source/mc/mvrtrn.src source/fcm/gcmc.fcm source/fcm/pbeq.fcm source/manip/scalar.src source/misc/gsbp.src source/misc/pbeq2.src ------------------------------------------------------------------------------ 1.11 University of Minnesota Developments Developers : Jingzhi Pu, Jiali Gao, and Donald G. Truhlar Email Address : pu@comp.chem.umn.edu Institution : University of Minnesota Date : July 2004 1.11.1 GHO Boundary Treatment for SCC-DFTB/MM The generalized hybrid orbital (GHO) method is implemented for the self-consistent-charge density-functional tight-binding (SCC-DFTB) theory and molecular mechanics (GHO-SCC-DFTB/MM). A full description of the algorithm is given in J. Phys. Chem. A 2004, 108, 5454. Several issues regarding the implementation are discussed below: The current GHO implementation for SCC-DFTB largely resembles the one for the semiempirical QM module in CHARMM. Therefore, a large majority of the data structure and basis transformation routines are the same and used. The new file source/fcm/stbgho.fcm has a large part of overlap with source/fcm/qmlink.fcm. Similarly, the new file source/sccdftbint/stbgho.src also contains some subroutines that have already been included in source/quantum/qmset.src. However, the multiple occurrence of these codes will not conflict with each other, because they are subjected to the conditional compilation options. Since the QUANTUM and the SCCDFTB module are mutually exclusive, only one set of these subroutines or common block data will be actually compiled. In GHO-SCC-DFTB, the torsion across the QM/MM boundary is treated somewhat differently than the case where a link atom is used. If we denote the GHO boundary atom as B and denote the QM atom bonded to the GHO boundary atom as A, the MM energy for X-A-B-X type torsions will be included in the total energy. For a link atom treatment, such MM torsions would be excluded from the total energy since both the central atoms are QM atoms. We prefer to retain the X-A-B-X torsions in the GHO method to obtain a more realistic rotational energy profile. The corresponding modification has been made in the file source/gener/update.src. Files Added: doc/sccdftb.doc source/sccdftbint/stbgho.src source/fcm/stbgho.fcm Files Modified: source/sccdftbint/sccdftbini.src source/sccdftbint/sccdftbsrc/eglcao.f source/sccdftbint/sccdftbsrc/gradient.f source/sccdftbint/sccdftbsrc/mulliken.f source/sccdftbint/sccdftbsrc/repulsive.f source/gener/update.src .............................................................................. 1.11.2 Recentering Bug fix A bug has been fixed for the reCENTering utility that allows to recenter the system at the geometric center of the first NCRES residues in the psf file. A redundant section of the code has been commented out. File Modified: source/dynamc/dcntr1.src .............................................................................. 1.11.3 MO Transformation Bug fixed In the GHO implementation for the semiempirical QM module, a bug has been fixed for the transformation of the molecular orbitals (MOs) from the hybrid orbital (HO) basis to the atomic orbital (AO) basis when more than one GHO boundary atoms are involved. Although this bug did not affect results of energies, gradients, and atomic Mulliken charges, it may potentially cause problems if the MOs (obtained from a multi-boundary GHO calculation) are further used by other routines for other purposes. File Modified: source/quantum/qmset.src ------------------------------------------------------------------------------ 1.12 SASA Changes and Enhancements Developers : Urs Haberthuer and Amedeo Caflisch Email Address : atlantis@bioc.unizh.ch, caflisch@bioc.unizh.ch Institution : University of Zurich, Switzerland Date : July 3, 2004 The keywords to modify the SASA parameters from within the CHARMM input file were changed for clearer usability. This concerns the keywords to modify the radii, probabilistic parameters, and connectivity parameters for the surface calculations. The keywords to modify the surface-tension like solvation parameters were also changed. See the SASA documentation for the new syntax. Two keywords, INFX and SURF, were added. INFX causes the fixed exclusion atoms to be considered for the surface calculations. (By default, they are neglected for historical reasons. See the SASA documentation for more detailed explanations.) SURF causes the approximated atomic solvent accessible surface areas to be stored in WMAIN. Lazaridis and coworkers introduced the CHARMM atom type CR in param19_eef1.inp and toph19_eef1.inp. This atom type is now considered explicitly in the SASA code although all the SASA parameters for CR are identical to those for the CHARMM atom type C. Some code cleanup and adjustments of the documentation within the SASA code were performed. Files Modified: doc/sasa.doc source/fcm/sasa.fcm source/misc/sasini.src source/misc/sasene.src =========================================================================== [2] c32a2 Change Log The following are introduced and modified during the development period of August 15, 2004 through February 15, 2005. The developments are based on CHARMM version c31a1. 2.1 Developments at University of Maryland Developers : Victor Anisimov, Denzil Bernard and Alex D. MacKerell, Jr. Email Address : victor@outerbanks.umaryland.edu bernard@outerbanks.umaryland.edu Institution : University of Maryland Date : December 27, 2004 2.1.1 Rotational, Translational and Vibrational Entropy Calculation of rotational, translational and vibrational entropy is added. The rotational and translational components are calculated in manip/rgyr.src and vibrational component of entropy is calculated in vibran/vibsub.src. Entropy keywords are read in manip/corman.src (as an extention to the COOR command) and in vibran/vibran.src (as an extension to VIBRan DIAG command). The VIBRan command is invoked to calculate all three entropy components (rotational, translational, and vibrational). VIBRAN will perform vibrational entropy calculation and will call CORINER subroutine to perform calculation of rotational and translational components. When invoked from the COOR command only rotational and translational entropy components will be calculated. Files Added: source/fcm/entropy.fcm Files Modified: source/manip/corman.src source/manip/rgyr.src source/vibran/vibran.src source/vibran/vibsub.src doc/corman.doc doc/vibran.doc doc/subst.doc New Testcase: test/c32test/entropy.inp .............................................................................. 2.1.2 ESP Charge Fitting and Drude Polarizability Determination Charge fitting capability is introduced into the misc module (with Guillaume Lamoureux). Files Added: source/misc/fitcharge.src Files Modified: source/charmm/charmm_main.src New Documentation: doc/fitcharge.doc New Testcase: test/c32test/cyt_chgfit.inp !CHARMM input file test/data/cyt_chgfit.pot !input data test/data/cyt_chgfit.pot0 !input data test/data/cyt_chgfit.qpos !input data .............................................................................. 2.1.3 Flexible Format for Printing Vibrational Frequencies Printing vibrational frequencies for a very large molecule causes format overflow in the field of "mode number" for systems larger than 3333 atoms. This is because the i4 format allows printing of 9999 modes only. To fix this problem a flexible format was implemented, which changes the format specification depending on the number of modes to print. The i4 format is kept for systems up to 3333 atoms. The extended format is aplied to larger systems changing the format specification based on number of modes to print. The printing function (subroutine) FREQPR is added to vibran/vibutil.src Files Modified: source/vibran/quasi.src source/vibran/rbquas.src source/vibran/redbas.src source/vibran/vibsub.src source/vibran/vibutil.src .............................................................................. 2.1.4 Numerical Vibrational Analysis with SCF Drudes Regular vibrational analysis treats Drude particles as real atoms and thus shows extra peaks on the IR-spectrum due to the Drude particles. This complicates CHARMM IR-spectrum comparison with QM or experimental data. The purpose of this addition is to allow vibrational spectrum analysis for molecules in the presence of Drude particles to be conducted in such a way that Drude particles will not be present in the IR-spectrum. This regimen is called SCF Drudes where the position of Drude particles is instantenously adjusted to any rearrangement in ithe position of real atoms. Second derivatives are calculated by using finite differences applied to real atoms and followed by Drude coordinate relaxation after every change in coordinates of real atoms. This way Drude degrees of freedom are projected onto the second derivatives of the real atoms. New logical variable LDSCF was introduced to VIBRAN subroutine. This keyword is set .TRUE. by presense of newly introduced DSCF keyword to VIBRAN as an extention to the DIAG subcommand. Since Drude particles are treated in the SCF regimen the mass assigned to Drude particles is moved back to the corresponding real atom. The initial masses of real atoms and Drude particles are backed up in the temporary array BAM having size BSPACE: Files Modified: source/vibran/vibran.src source/vibran/vibsub.src source/vibran/raise.src source/vibran/vibcom.src doc/vibran.doc New Testcase: test/c32test/dscfvib.inp .............................................................................. 2.1.5 MOLVIB Analysis with Drudes Regular MOLVIB analysis does not support the classical Drude oscillator polarizable model. The support was added by calculating numerical second derivatives under the condition of SCF Drudes and passing the resized second derivative matrix and coordinates and masses of real atoms to the MOLVIB subroutine. This approach is invoked automatically in the presence of Drude particles. Files Modified: source/molvib/molvco.src source/molvib/molvsb.src doc/molvib.doc New Testcase: test/c32test/dmolvib.inp .............................................................................. 2.1.6 COOR MAXDIST The command computes the MAXIMUM distance between two selected sets of atoms. Similar to the COOR MINDIST command. Calls to SUBROUTINE DISTAN have been modified to include an additional logical variable MAXD Files Modified: manip/corman.src manip/corman3.src doc/corman.doc ------------------------------------------------------------------------------ 2.2 TSRI Developments Developers : Mike Crowley and Charles L. Brooks, III Email Address : crowley@sripps.edu, brooks@scripps.edu Institution : The Scripps Research Institute Date : December 30, 2004 2.2.1 AFM Reset The reset command is added to afm. This permits the afm commend to be run in a loop with all data structures cleared in between. Files modified: doc/afm.doc source/energy/afm.src source/fcm/afm.fcm .............................................................................. 2.2.2 Clean-Up Some code cleanup and prefx labeling to make debugging easier. Files modified: source/energy/energy.src source/energy/eutil.src source/nbonds/enbfast.src source/util/prpref.src .............................................................................. 2.2.3 GBMV Bugfix We fixed a number of issues related to the performance and correctness of the GBMV code on serial and parallel machines. Files modified: source/energy/gbmv.src source/fcm/gbmv.fcm .............................................................................. 2.2.4 Huge Version HUGE keysord added to code and install.com for million atom systems. Files modified: install.com source/fcm/dimens.fcm source/fcm/heap.fcm source/fcm/stack.fcm .............................................................................. 2.2.5 Makefile Update Updated osx and gnu Makefiles Files modified: build/UNX/Makefile_osx build/UNX/Makefile_gnu .............................................................................. 2.2.6 Testcase Fixes Small fixes to test cases to correct poor design of some test cases and to add some functionality to others. Files modified: test/c31test/nebdiala.inp test/c31test/afm.inp test/c31test/nebdialapmf.inp test/c31test/off_path_simulation.inp .............................................................................. 2.2.7 Timing Fixes Timer debugging added to prevent double timing and other timing errors. Files modified: source/fcm/new_time.fcm source/util/new_timer.src ------------------------------------------------------------------------------ 2.3 Developments at the National Institute of Health Developers : H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks Email Address : hlwood@nih.gov, wuxw@nhlbi.nih.gov, brb@nih.gov Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH Date : December 20, 2004 2.3.1 Molecular Modeling with Map Objects The EMAP module is expanded to energy-based map object modeling. The concept of field maps is introduced to describe electrostatic field of a molecular system. The field map and density map, as well as the core map provide a way to evaluate energies between map objects. Based on energies, map objects can be used to search low energy conformations of macromolecular assemblies. Files Added: source/emap/emapfield.src Files Modified: source/fcm/emap.fcm source/emap/emapsubs.src source/emap/emapop.src source/emap/emapdock.src source/emap/emapio.c doc/emap.doc doc/io.doc New Testcase: test/c32test/dock_with_maps.inp test/data/tcr.pdb .............................................................................. 2.3.2 IPS Enhancement for 2D Homogenous Systems IPS pressure tensions are calculated based on homogenous directions for surface tension calculation. 2D IPS routines are added for faster calculation. Files Modified: source/fcm/nbips.fcm source/energy/energy.src source/nbonds/enbond.src source/nbonds/enbips.src source/nbonds/nbutil.src source/nbonds/pmeutil.src doc/nbonds.doc test/c32test/ips_tip216.inp .............................................................................. 2.3.3 SGLD Improvements The guiding force calculation in routine SGLDW is improved. An input parameter, TEMPSG, is added SGLD algorithm for MD simulation is added as SGMD Files Modified: source/fcm/sgld.fcm source/dynamc/sglds.src source/dynamc/dcntrl.src source/dynamc/dynamc.src doc/sgld.doc test/c31test/sgld.inp .............................................................................. 2.3.4 Replica Path and Off-Path Simulation Enhancements (Lee Woodcock and Milan Hodoscek) Defined maximum number of replicas allowed (1000). Added the ability to restart off-path simulations from previous run. Must use restart file for this. Once off-path simulations is done potential of mean force is written out to a file (pmf.dat). Files Modified: source/energy/epath.src source/fcm/path.fcm source/dynamc/dynio.src .............................................................................. 2.3.5 QM/MM Improvements 1. Added noguess option to running parallel replica path with Q-Chem 2. Removed obsolete variables and comments 3. Fixed QM force manipulation 4. Fixed SCF convergence error printing 5. Fixed Sodium definition in Findel (Lee and Milan) Files Modified: source/gukint/gukini.src source/quantum/addlnat.src source/fcm/gamess.fcm .............................................................................. 2.3.6 Free Energy Perturbation Bug Fixes 1. Fixed data structure problem: SPPSFT was not being set properly 2. Added memory allocation and correct filling for things defined in the data structures Files Modified: source/pert/pert.src source/fcm/pert.fcm .............................................................................. 2.3.7 Added QM/MM Free Energy Pertubation (with Q-Chem) 1. Added Mass to PERT data structure 2. Modified GUKENE and QCHEM subroutines and calls 3. Added QM/MM energy calls to epert routines 4. Fixed QCHEM subroutine to use both lambda 0 and lambda 1 PSF 5. Added XX as an atom type to Findel: this represents a quantum dummy atom 6. Added test case for QM/MM free energy perturbation Files Modified: source/gukint/gukini.src source/nbonds/nbonds.src source/quantum/addlnat.src source/energy/energy.src source/pert/epert.src source/pert/pert.src source/fcm/pert.fcm Files Added: test/cquantumtest/qmmm_pert.inp test/data/qmmm_pert.inp test/data/s0.inp test/data/s1.inp ------------------------------------------------------------------------------ 2.4 Developments at NIC-Slovenia Names : Milan Hodoscek Email Address : milan@cmm.ki.si Institution : National Institutes of Chemistry, Ljubljana, Slovenia Date : December 30, 2004 2.4.1 New Reaction Coordinate added to Biased MD The helix expansion reaction coordinate was added to the HQBM module. Files modified: source/energy/hqbm.src source/fcm/hqbm.fcm 2.4.2 Replica Path fixes. The problem with parallel and scalar QM/MM replica path method is fixed Files modified: source/energy/ecnstr.src source/energy/epath.src source/fcm/parallel.fcm source/machdep/paral1.src 2.4.3 GAMESS QM/MM DFT speedup The new GAMESS DFT SCF convergency enhancement is switched off when using NOGUess keyword, which significantly speeds up the calculations. Files modified: source/fcm/gamess.fcm source/gukint/gukini.src 2.4.4 New version of GAMESS is supported in CHARMM Version of GAMESS 22 November 2004 R1 is now supported with CHARMM. New in this version are faster two electron integral code, and QFMM derivatives. Files modified: source/gamint/ddi.src source/gamint/gamess/gamess.src source/gamint/gamess/grd1.src source/gamint/gamess/grd2a.src source/gamint/gamess/guess.src source/gamint/gamess/inputa.src source/gamint/gamess/inputb.src source/gamint/gamess/inputc.src source/gamint/gamess/int1.src source/gamint/gamess/iolib.src source/gamint/gamess/mccas.src source/gamint/gamess/prpel.src source/gamint/gamess/prplib.src source/gamint/gamess/prppop.src source/gamint/gamess/rhfuhf.src source/gamint/gamess/scflib.src source/gamint/gamess/unport.src 2.4.5 LONEPAIR in PSF fix If LONEPAIR is not specified in pref.dat psfres.src doesn't compile. Also reading PSF files in this case was not correct. Fixed now. Files modified: source/io/psfres.src 2.4.6 Parallel fixes Debug output removed in paral2.src. Some machines can't compile TCP/IP socket code, so it is removed unless specified in pref.dat Some parallel libraries don't remove the command line parameters. There can be more than 30 so maximum is increased to 300 Files modified: source/machdep/paral2.src source/machdep/socket.c source/machdep/startup.src install.com 2.4.7 Writing of the trajectories from MINI CONJ Support to write trajectory files from MINI CONJ calculations. Mainly used for QM/MM. Files modified: source/minmiz/conjug.src ------------------------------------------------------------------------------ 2.5 Developments at Cornell University Developers : Yuqing Deng, Guillaume Lamoureux, Igor V. Vorobyov and Benoit Roux Email Address : yud2001@med.cornell.edu, Guillaume.Lamoureux@cornell.edu benoit.roux@med.cornell.edu Institution : Weill Medical College of Cornell Univeristy Date : December 21, 2004 2.5.1 WCA Separation of LJ potential The LJ potential is spit into repulsive and attractive parts in EGROUP. Three addition arguments are added to EGROUP. A new scalar WCAD is introduced in the PSF, which is used to scale the WCA-attractive potential. The manipulation of WCAD is implemented analogous to RSCALF. Two logicals (scl0, scl1) and floating point arguments (scr0, scr1) are introduced in the PERT command line for progressively turning on WCA-repulsion in free energy calcualtion. Two arguments (EMP1, EMP2) are introduced in the SSBP MMFP command line for empirical correction of SSBP. The empirical correction can be turned on and off with EMPI and NEMP, respectively. PERT command stores the selected atoms (in PERT command line) in an array and these are used in EPERT to calculate long-range correction for SSBP free energy. Three miscellaneous energy variables are added: WHAMFE, total free energy of WHAM SSBPLRC, long-range free energy correction for SSBP SSBPLRCS, standard deviation of SSBP long-range correction Files Modified: source/charmm/charmm_main.src source/charmm/iniall.src source/emap/emapsubs.src source/energy/energy.src source/energy/intere.src source/fcm/dimens.fcm source/fcm/pert.fcm source/fcm/psf.fcm source/fcm/ssbp.fcm source/gener/drude.src source/gener/genpsf.src source/gener/modpsf.src source/gener/replica.src source/image/eimage.src source/image/upimag.src source/io/psfres.src source/manip/scalar.src source/mbond/mbdiag.src source/mc/mcener.src source/mc/mcimge.src source/misc/ssbp.src source/misc/xray.src source/nbonds/enbond.src source/nbonds/enbondg.src source/pert/epert.src source/pert/icfcnf.src source/pert/icpert.src source/pert/pert.src source/pert/tsme.src source/pert/wham.src source/quantum/addlnat.src source/quantum/qmene.src source/shapes/mdlio.src source/util/selcta.src source/vibran/vibblock.src doc/mmfp.doc doc/pert.doc doc/scalar.doc doc/subst.doc New Testcase: test/c32test/attr.inp test/c32test/repul.inp test/data/pert.prt .............................................................................. 2.5.2 Code Cleanup and Bug Fixes in TPCONTROL and DYNA VV2 For constant-pressure simulations containing Drude oscillators, the TPCONTROL command is now scaling the Drude--atom distances (i.e., the dipoles) along with all other bonds. This behavior could be obtained in the previous version of the code by using the non-documented "DSCY" flag, but it was not the default. (BUGFIX, tpcontrol.src) The dimensions of the crystal cell (?XTLA, ?XTLB, ?XTLC) were not updated after a call to DYNA VV2. (BUGFIX, dcntrl.src) are. Some inessential parts of the VV2 subroutine were never fully functional. They have been removed. (CODE CLEANUP, dynamvv2.src) The SCF treatment of Drude oscillators implemented for DYNA LANG was "forgetting" the special nature of Drude particles after exiting the DYNAMC subroutine, resulting in a crash at restart. (BUGFIX, dynamc.src) Files Modified: source/dynamc/dcntrl.src source/dynamc/dynamc.src source/dynamc/dynamvv2.src source/dynamc/tpcontrol.src ------------------------------------------------------------------------------ 2.6 Karolinska Institute Fixes and Enhancements Developer : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : December 30, 2004 2.6.1 Minor modifications/fixes (1) SINGLE precision version cannot be created due to use of non-generic forms of intrinsic functions in several routines. I updated prefx.src with these, and also had to make some changes to source files. CHARMM created with SINGLE in pref.dat is however NOT fully functional. Timing routines (elapsed time) do not work, parallel jobs hang (I only tried socket communication), charges do not sum up correctly at psf generation; there may be other problems as well. It would be useful to have this working correctly again. Files modified: tool/prefx.src source/adumb/eadumb.src source/emap/emapdock.src source/util/selcta.src (2) Set values of BOMLEV, IOLEV, PRNLEV variables at startup, corrected a typo in FTCPWRT call Files modified: source/charmm/charmm_main.src (3) Added SURFace-area timeseries to correl.src and allow output of long lines to data files if LONG command is in effect. Files modified: source/correl/correl.src source/correl/anacor.src source/correl/corrio.src source/manip/corman.src source/misc/surfac.src doc/correl.doc (4) Allow echeck to be turned off by specifying a negative value; not documented. Files modified: source/dynamc/dynamc.src (5) Some format changes to allow for large step numbers to print correctly. Files modified: source/dynamc/dynsub.src (6) Format change to allow larger heap allocations to be correctly reported. Files modified: source/machdep/space.src (7) Collect histograms of hydrogen-bond length and lifetime distributions in COOR HBOND. Files modified: source/manip/hbanal.src doc/corman.doc Files added: source/fcm/hbanal.fcm (8) Modification of log-file handling in install.com to log the output from the current compile/link to build//new.log, which is appended to build//.log. Files modified: install.com (9) Added keyword DEBUG to install.com - this sets enviroment variable DEBUG, which is parsed by Makefile_gnu to use the debugging definition of the compile command FCD. Files modified: install.com build/UNX/Makefile_gnu (also contains some intel fortran flag changes) .............................................................................. 2.6.2 SOLVENT-SOLVENT interaction routine Experimental water-water interaction routine for CHARMM c32a1. Depending on the size of the system and the number of water molecules, speedups in the range of 2-5 fold may be obtained. Non-bonded interactions within a user specifed selection of water molecules (any three site water model with the oxygen first in the PSF should work) are removed from the regular non-bonded lists and are instead handled by a dedicated routine. Pref.dat The code is protected by keyword SLVSLV Modified files: source/energy/energy.src source/image/upimag.src source/image/eimage.src source/charmm/miscom.src source/charmm/iniall.src source/nbonds/nbonds.src build/gnu/nbonds.mk incomplete, just compiles ewwnb.src, but there are no checks on wwnb.fcm doc/nbonds.doc New files: source/nbonds/ewwnb.src routines for setup, space allocation, and the energy calculation source/fcm/wwnb.fcm test/c32test/nbsolv.inp test/output/nbsolv.out output from nbsolv.inp using c32a1 ifort v8 on RH9 GNU/Linux .............................................................................. 2.6.3 Partial Table Lookup For the distance dependent parts of the Coulomb and van der Waals forces, for all interactions. Moderate speedup (10-20%). Protected by LNTAB1 in pref.dat. Files modified: source/charmm/iniall.src source/energy/energy.src source/nbonds/enbaexp.src source/nbonds/nbutil.src source/nbonds/nbonds.src doc/nbonds.doc New files: source/nbonds/ewwnb.src sourc/fcm/wwnb1.fcm ------------------------------------------------------------------------------ 2.7 Multiple and Moving Point NOEs Name : Michael Schaefer Email Address : michael.schaefer@syngenta.com Institution : Syngenta Crop Protection AG, Basel Date : 27.12.2004 The previous PNOE implementation would allow for a single point-NOE only (an NOE between an atom or group of atoms, and a single point in space). This has been generalized to allow for multiple point-NOE's, just like normal atom(group) -- atom(group) NOE's. The documentation does not require change in this respect, as it appeared to suggest that multiple PNOE's are possible. To further enhance the capabilities offered by the PNOE scheme, the NOE facility now offers the option of moving point-NOE's, with a predefined set of of starting points, target points, and a number of dynamics or minimization steps over which the PNOE's are to move. Minor bugs related to PNOE's have been fixed, e.g., the distribution of data to all nodes in parallel mode, or the read/write of NOE data concernign PNOE's where the J-atom list is irrelevant (it is a point). Files Modified: source/adumb/eadumb.src source/charmm/iniall.src source/energy/energy.src source/fcm/noe.fcm source/mc/mc.src source/mc/mcener.src source/misc/genetic.src source/misc/noe.src source/pert/epert.src doc/cons.doc New Testcase: test/c32test/pnoe.inp ------------------------------------------------------------------------------ 2.8 SASA Enhancements and Bugfixes Developers : Urs Haberthuer, Riccardo Pellarin, and Amedeo Caflisch Email Address : atlantis@bioc.unizh.ch, pellarin@bioc.unizh.ch, caflisch@bioc.unizh.ch Institution : University of Zurich, Switzerland Date : December 30, 2004 (1) New Surface Parameters A new keyword, NEWP, is added. It triggers the use of a new set of values for the radii, probabilistic parameters, and connectivity parameters. (These parameters are used to calculate atomic solvent accessible surface areas within the SASA module.) The new set was derived in 2002 by Haberthuer and it gives a better correlation with exact analytical surfaces than the original Hasel and Still surface parameters. (2) Images Image lists are now supported in SASA. This allows to use SASA for simulations with periodic boundary conditions. (3) Documentation The SASA documentation itself and also the documentation within the SASA code is updated. (4) Miscellaneous The atom type C1ES is now supported by SASA and the format of the output of the SASA module slightly changed. (5) Bugfixes The SASA module did not work correctly for simulations with constant pressure since the call to the subroutine SASENE in the subroutine ENERGY was at the wrong place. This has been corrected. An empty nonbond exclusion pair list could crash the SASA module. This bug is now fixed. Files Modified: doc/sasa.doc source/energy/energy.src source/fcm/sasa.fcm source/misc/sasini.src source/misc/sasene.src ============================================================================== [3] c32b1 Change Log The following are enhancements and bugfixes of the development period from February 15, 2005 through August 15, 2005. The developments are based on CHARMM version c32a2. 3.1 General compilation of SCC-DFTB in CHARMM Developers : Qiang Cui Email Address : cui@chem.wisc.edu Institution : University of Wisconsin, Madison Date : July 1, 2005 "$(LIB)/sccdftbint.a" is added to all platform Makefiles of build/UNX. Otherwise, SCC-DFTB will NOT be compiled even with the T keyword. Files Modified: install.com ------------------------------------------------------------------------------ 3.2 TSRI Cleanup and Bugfixes Developers : Mike Crowley, Charles L. Brooks, III Email Address : crowley@sripps.edu, brooks@scripps.edu Institution : The Scripps Research Institute Date : June 30, 2005 Files Modified: source/dynamc/dynamc.src some pref labels added source/emap/emapfield.src removed extraneous "+" characters and fixed heap call source/energy/gbmv.src bugfixes source/fcm/gbmv.fcm bugfixes source/gener/mkpres.src bugfix format statement source/io/rtfio.src very minor cleanup source/manip/shake.src cleanup and remove PARASCAL code for fast shake source/manipfsshake.src source/misc/mmfp.src bugfix format statement source/misc/pbeq.src bugfix format statements ------------------------------------------------------------------------------ 3.3 Developments at the National Institute of Health Developers : Jhih-Wei Chu, H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks Email Address : chu@hec.utah.edu, hlwood@nih.gov, wuxw@nhlbi.nih.gov, brb@nih.gov Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH Date : July 1, 2005 3.3.1 NEB minimization problem fix The SD code is modified so that it can be used with NEB. "If(QPNEB)" is used to separate the NEB related code and the original part. NEB related parts in epath.src and energy.src are modified to make sure the NEB method works (the NEBF command). Warning added when NEB+climbing image is used together in ABNR. Files Modified: source/energy/energy.src source/energy/epath.src source/minmiz/steepd.src source/minmiz/abnr.src Modified Documentation: doc/minmiz.doc doc/replica.doc .............................................................................. 3.3.2 IPS Bugfix For partial homogenous systems (2D as PXY or 1D as PZ), the boundary energies and forces need to be calculated, which was done by looping over all atom pairs and is slow. A speed up was done by calculating boundary forces every NIPSFRQ steps. However, a large NIPSFRQ introduces large errors in the calculation results. This fix changes the way in which boundary energies and forces are calculated so that the calculation is very efficient and can be done every dynamcs step without significantly slowing down a simulation. NIPSFRQ is set to 1 by default and can be set to large values for simulations where conformational change is slow. Files involved: source/fcm/nbips.fcm Updated common variables source/energy/energy.src Modified parallelization for EXIPS, EXIPS2D, and EXIPS3D calculation. source/nbonds/enbond.src Changes in ENBIPS2D arguments. source/nbonds/enbonda.src Common variable updates. source/nbonds/enbondg.src Common variable updates. source/nbonds/enbfast.src Common variable updates. source/nbonds/enbips.src Change the way in which IPSSYS and IPSSYS2D is calculated. source/quantum/qmene.src Change to make consistant in ENBOND arguments. ------------------------------------------------------------------------------ 3.4 IBM Pwr4 Port Names : Milan Hodoscek Email Address : milan@cmm.ki.si Institution : National Institutes of Chemistry, Ljubljana, Slovenia Date : June 30, 2004 Support for parallel CHARMM on IBM power4 CPU architecture using GNU/Linux as an operating system. Files Added: build/UNX/Makefile_ibmlnxmp tool/ibmlnxmp_fixlibs Files Modified: source/energy/rmsd.src source/machdep/cstuff.c - one #if source/machdep/machio.src - order changed for ##IF doc/parallel.doc install.com ------------------------------------------------------------------------------ 3.5 Developments at Cornell University Developers : Edward Harder, Hyung-June Woo, Jose D. Faraldo-Gomez, Yuqing Deng, Benoit Roux Email Address : edh2004@med.cornell.edu, woo@chem.unr.edu, jdf2002@med.cornell.edu, yud2001@med.cornell.edu, benoit.roux@med.cornell.edu Institution : Weill Cornell Medical College Date : June 25, 2005 3.5.1 The Drude mass dependence bugfix This fixes bugs for the Drude mass dependance when using SCF dynamics and another bug for restarting of VV2 dynamics in the NVE ensemble. When simulating drude models using the SCF evaluation of the drude particle positions (drude mass independant) the trajectories were dependent on the drude mass. Also, VV2 dynamics using no thermostat and no barostat couldn't be restarted. Subroutine READYN would complain about an "EOF during read". Files involved: source/dynamc/dcntrl.src source/dynamc/dynamc.src .............................................................................. 3.5.2 Dipole time series bugfix Dipole time series produced is incorrect for use in the calculation of the dielectric constant. If MAXA is not set in the input file the default maximum atom selection is arbitrarily set to 100 which is often insufficient for calculating bulk dipole moment time series. To fix this the default value has been set to the number of atoms in the system "NATOM". Files involved: source/correl/correl.src ------------------------------------------------------------------------------ 3.6 Karolinska Institute Fixes and Enhancements Developer : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : June 30, 2005 1) Modification. Allow a subset of a timeseries to be copied in CORREL MANTIM COPY. Files Modified: source/correl/mantim.src doc/correl.doc 2) Bugfix: Calling sequence to ALLHP wrong in emapfield.src File modified: source/emap/emapfield.src 3) Bugifx: Protect parllel comm call from being executed when not needed. ECONT array only needs to be distributed when QECONT is true. Files Modified: source/energy/energy.src 4) Bugfix: Coding error for the new RECT crystal type. Files Modified: source/image/crystal.src) 5) Bugfix. Array dimensions were wrong, and part of the logic flawed for the check that the main axis did not swap direction 180 degrees, in the code to return all three axes for the inertial moment timeseries (ENTER ... INER ALL). Some new code added to check for axis swap for the other two axes as well. Files Modified: source/correl/anacor.src doc/correl.doc 6) Minor modifications. Files Modified: install.com Updated options for SCALI; set chmsocket for cc as well as gcc when needed source/nbonds/ewwnb.src Output format change in informational message doc/io.doc Clarification of WRITE/PRINT NBOND and keyword FIRST for WRITE COOR PDB FIRST test/c32test/dscfvib.inp Corrected erroneous use of ?vibran .ne. 1 test/c32test/entropy.inp (should be ?novibran .eq. 1) ------------------------------------------------------------------------------ 3.7 University of Chicago Bugfixes Developers : Aaron R. Dinner Email Address : dinner@uchicago.edu Institution : The University of Chicago Date : June 30, 2004 (1) Memory allocation error fix Scratch arrays are allocated for charge equilbration during the DYNAMC call but not freed. In addition to memory leak, arrays are allocated as HEAP then used as STACK. Files involved: source/mc/mvhmc.src (2) RXNCOR fix Forces but not energies from umbrella potential term are added to totals. Umbrella potential term is not added to total energy or printed. Added UMBR to ETERM array and made corresponding changes in energy utilities. Files involved: source/energy/energy.src source/energy/eutil.src source/energy/printe.src source/fcm/energy.fcm source/fcm/rxncom.fcm source/rxncor/rxnene.src (3) MC fix for MVTYP GCMC and GRID/CBIAS Error-check for no blockers is done before counting them. Files involved: source/mc/mvgcmc.src (4) GCMC counter fix GCMC counters not updated when runnning with finite rather than periodic boundary. Files involved: source/mc/mcener.src ------------------------------------------------------------------------------ 3.8 University of Maryland, School of Pharmacy Developments Developers : Alex MacKerell, Igor Vorobyov, Victor Anisimov Pedro Lopes Email Address : alex@outerbanks.umaryland.edu Institution : University of Maryland, School of Pharmacy Date : July 14, 2005 3.8.1 Parameters for classical Drude oscillator model. Force field parameters for the developmental polarizable model based on a classical Drude oscillator have been added. Currently, only parameters for the SWM4-DP water models, alkanes and ions are available. Toppar files along with example inputs are in the toppar/drude directory. 3.8.2 Parameters for silicate surfaces. Force field parameters for silicate and aluminosilicate surfaces are now availble in the toppar/silicate directory. Included are code and example inputs to create and generate a quartz 001 surface. Note that these parameters have been designed to be compatible with the CHARMM22 and 27 all-atom force fields. Documentation available in parmfile.doc ------------------------------------------------------------------------------ 3.9 Minor Enhancements and Fixes 3.9.1 SPCISM update Developer : Sergio A. Hassan Email Address : mago@helix.nih.gov Institution : CMM/DCB/CIT, National Institutes of Health (NIH) Date : June 16, 2005 SCPISM doc is updated File Involved: doc/scpism.doc .............................................................................. 3.9.2 IMM1 Testcase Updated Developer : Themis Lazaridis Email Address : tlazaridis@ccny.cuny.edu Institution : City College of New York/CUNY Date : July 12, 2005 The testcase include checking the energy against the expected value. File Involved: test/c31test/testimm1.inp .............................................................................. 3.9.3 SHELL Bugfix Developers : Tibor Rudas, Stefan Boresch Email Address : tibi@mdy.univie.ac.at, stefan@mdy.univie.ac.at Institution : Molecular Dynamics and Biomolecular Simulation group at the Department of Biomolecular Structural Chemistry, University of Vienna Date : June 28, 2005 If solvent is decomposed into shells around a solute with shells extending to less than 8A or to more than 20A the cube size for the cubing based algorithm is reset. In the former case this leads (only) to a less efficient - but correct - decomposition while the generated shells can be incomplete in the latter case. Files involved: source/correl/shell.src .............................................................................. 3.9.4 SASA Segmentation Fault Error Fixed Developers : Riccardo Pellarin and Amedeo Caflisch Email Address : pellarin@bioc.unizh.ch, caflisch@bioc.unizh.ch Institution : University of Zuerich, Switzerland Date : June 21, 2005 When one tries to simulate a sequence that does not contain any TRP or PHE or TYR, (or in any case where the nonbond explicit exclusion list is empty) one would get a segmentation fault immediately after the command call. As an output the following instance error message is normally obtained: FREHP> sasini.src/SASINI releases 66 words of PXBL at ********** BAD BASE, ********* OR LEN2, 66 PASSED TO FREEHP However we experienced, in some machines and in some particular compilations, that program prints only "segmentation fault" or even stops without any alert. Files involved: source/misc/sasini.src .............................................................................. 3.9.5 PERT MD Simulation Fix Developer : Stefan Boresch Email Address : stefan@mdy.univie.ac.at Institution : University of Vienna Date : July 18, 2005 PERT MD runs die with error "GENERATING TOO MANY IM CONTACTS". Use of PERT automatically disables the BYCB method. Thus, no BYCB only code should be executed. However, the error message "GENERATING TOO MANY IM CONTACTS" is triggered by a sanity check of the BYCB method, which shouldn't be active in PERT. The code in questions is protected by an ##IF IMCUBES block, but not protected against being executed if BYCB isn't used (such as is always the case in PERT runs). Files involved: source/nbonds/nbonds.src .............................................................................. 3.9.6 CHARMM Manager's Note 1) SPASIBA force filed code removed This was not released with c31b1 of August 15, 2004. As it has not been fixed nor verified, it is not included in the c32b release versions. 2) NBIPS is the default feature of c32b. ============================================================================== [4] c32b2 Change Log The following are enhancements and bugfixes of the development period from August 15, 2005 through February 15, 2006. 4.1 TSRI Cleanup and Bugfixes Developers : Mike Crowley, Charles L. Brooks, III Email Address : crowley@sripps.edu, brooks@scripps.edu Institution : The Scripps Research Institute Date : December 31, 2005 - Timer fixes to solve the double-counting problem - Timer debugging code to check if double-counting or incorrect counting is suspected - integer*4 binary I/O enforced. - f90 compile for sgi IRIX fixes (SFIF90) [Note: This fails to compile on SGI and is removed. - chmgr ] - attempt to fix some of the memory hog problems using heap - Esoteric mpi code for supercomputer center installations: mpif90 support, memory hog bandaids, eliminate COPYR8, MPI INPLACE - HUGE size adjustments Files Added: build/UNX/Makefile_em64t build/UNX/Makefile_itanium Files Modified: build/UNX/Makefile_gnu build/UNX/Makefile_ibmaix build/UNX/Makefile_ibmaixmp build/UNX/Makefile_osx doc/cheq.doc source/cff/parrdr_cff.src i4 binary source/correl/solana.src SGIF90 source/dynamc/cveloci.src memory hog fix use heap source/dynamc/dynamc.src Timer fixes, mpiall, cheq source/dynamc/dynio.src i4binary fix source/dynamc/mts.src memory hog source/energy/energy.src timer fixes,mpiall source/energy/epath.src SGIF90 source/energy/eutil.src timer fix source/energy/gbmv.src SGIF90 source/energy/hqbm.src memory hog source/fcm/cveloci.fcm memory hog source/fcm/gbmv.fcm declaration fix source/fcm/new_time.fcm timer fixes source/fcm/pme_par.fcm increase node limit to 512 for parallel pme source/fcm/stack.fcm HUGE size adjustment source/image/upimag.src extra info for bomb from exceeding limits source/io/psfres.src CHEQ bug fixes source/machdep/machutil.src bug fixes, added support for using mpif90 instead of specific compiler name so it will find mpif.h, support for ia64 mpi source/machdep/paral1.src mpif90 source/machdep/paral2.src mpif90 source/machdep/paral3.src mpif90 source/machdep/startup.src change for HUGE and itanium header source/manip/shake.src size overflow protection and mpif90 source/minmiz/abner.src ##IF fix source/misc/surfac.src size HUGE added source/nbonds/enbond.src timer fix source/nbonds/ewald.src CHEQ fix source/nbonds/nbutil.src memory hog bandaid source/nbonds/pmeutil.src node limit increased, mpif90 support source/util/new_timer.src timer debugging added source/util/title.src testendian fixes ------------------------------------------------------------------------------ 4.2 Developments at the National Institute of Health Developers : H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks Email Address : hlwood@nih.gov, wuxw@nhlbi.nih.gov, brb@nih.gov Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH Date : December 31, 2005 4.2.1 EMAP I/O and Command fixes The CCP4 map head data format is corrected. Map operation bugs are fixed Files involved: source/emap/emapio.c source/emap/emapop.src source/emap/emapsubs.src source/emap/emapdock.src source/fcm/emap.fcm doc/emap.doc .............................................................................. 4.4.2 Bugfix for guiding temperature calculation Guiding temperature calcuation is corrected based on friction costant, local average time, and local average of guiding force products. Files involved: source/dynamc/dcntrl.src source/dynamc/dynamc.src source/dynamc/sglds.src source/fcm/sgld.fcm test/c31test/sgld.inp doc/sgld.doc .............................................................................. 4.2.3 QM/MM Q-Chem interface Point charge gradient were being ignored if they occured after the QM region in the psf. This was fixed. Also, fixed a bug associated with how Q-Chem/CHARMM handled MP2 and RIMP2 QM calculations. Files involved: source/fcm/gamess.fcm Added stuff to handle RIMP2 QM calculations source/gukint/gukini.src Fixed reading of point charge gradients. .............................................................................. 4.2.4 image and nonbond commands The problem is that when using 'cons fix' some atoms non-bonded interactions (with other fixed atoms) are still computed even when they are fixed. In particular, in the first bug the loop which identifies atoms that are fixed misses the first fixed atom of each group, in the second bug the 'expand' option is not correctly conditioned on 'imove'. Files involved: source/nbonds/nbonda.src Added imove to the expand keyword test source/image/nbondm.src Set QMOVE to true ------------------------------------------------------------------------------ 4.3 Karolinska Institute Fixes and Enhancements Developer : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : December 30, 2005 4.3.1 64-bit space allocation From Bogdan's report. Files involved: source/machdep/space.src .............................................................................. 4.3.2 Bugfixes 1) The DONOr/ACCEptor commands did not work correctly in ADD mode. Also clarified documentation. Files involved: source/gener/hbonds.src doc/hbonds.doc 2) The code to correct inadvertent reordering of the minor inertial axes in CORREL timeseries INERtia ALL has been corrected. Files involved: source/correl/anacor.src 3) Fix the workings of selections and orientating structures in CORREL timeserise RMS Files involved: doc/correl.doc 4) Fast SHAKE bugfix (charmm.org) Files involved: source/manip/fsshake.src 5) PERT SSBP long range correction bugfix (charmm.org) Files involved: source/pert/pert.src