--------------------------------------------------------------------------- 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 CHARMM 30.0 c30a1 Developmental August 15, 2002 --------------------------------------------------------------------------- [0] About CHARMM30 Development As an on-going project, CHARMM development will be carried out with CHARMM version 30 series. The base revision is the beta release version c29b0. c30a1 is the first revision in the c30 developmental versions. The following describes new features and enhancements incorporated in the c30 development period. =========================================================================== [1] c30a1 Change Log The following are introduced and modified during the development period of April 15, 2002 through August 15, 2002. 1.1 Nudged Elastic Band Method Name : Paul Maragakis Email Address : maragakis@cmt.harvard.edu Institution : Harvard University Date : June 27, 2002 We added the nudged elastic band (NEB) approach to the replica path. In the NEB, one projects the spring forces along the path and the potential forces perpendicular to the path. It is one of the methods of choice for a quick and dirty approximation to the minimum energy path. Because of the projection of the forces there is no exact energy functional so that the NEB does not pass TEST1. We introduced two new keywords to the RPATH command: The keyword NEBA that activates the projections. The keyword KNEB that is the spring constant for the NEB method. It is possible to mix the other RPATH springs (e.g. KANG) with the NEB. Files Modified: source/energy/epath.src /fcm/path.fcm doc/replica.doc New Testcase: test/c30test/nebtest.inp ------------------------------------------------------------------------------ 1.2 Structural overlap method by using Gaussian overlap integrals Names : Milan Hodoscek Email Address : milan@cmm.ki.si Institution : National Institutes of Chemstry, Ljubljana, Slovenia Date : July 9, 2002 This is a maximum overlap method to investigate the structural similarity of flexible molecules. The atoms are described as Gaussians and the interaction energy between different molecules are basically overlap integrals. The Gaussians can represent either volume or charge. Alternatively, the overlap of the electrostatic potential is provided yielding exponential form. The method is enabled by OVERLAP pref.dat keyword Files Modified: source/charmm/charmm_main.src, iniall.src /energy/energy.src, eutil.src, printe.src /fcm/energy.fcm /util/prpref.src New Files: source/misc/olap.src /energy/eolap.src /fcm/olap.src doc/overlap.doc test/c30test/overlap.inp ------------------------------------------------------------------------------ 1.3 TSRI Developments Name : Michael S. Lee, Michael Feig, Mike Crowley and Charles L. Brooks, III Email Address : crowley@scripps.edu, brooks@scripps.edu Institution : TSRI Date : july 10 2002 1.3.1 Two-dihedral cross term based on interpolated grid map pref keyword: CMAP Files Modified: install.com source/charmm/charmm_main.src, iniall.src /correl/correl.src /dynamc/dcntrl.src, dynamln.src, dynio.src, mts.src, trnphi.src /energy/ecntrl.src, ediff.src, eintern.src, energy.src, eutil.src /intere.src, printe.src /fcm/block.fcm, code.fcm, dimens.fcm, energy.fcm, exfunc.fcm /image.fcm, param.fcm, pert.fcm, psf.fcm, rtf.fcm, tbmtsp.fcm /tsmh.fcm /flucq/flucq.src /gener/genpsf.src, modpsf.src, psfsum.src, replica.src, update.src /image/eimage.src, images.src, imagio.src, upimag.src /io/mainio.src, psfres.src, rtfio.src /manip/cstran.src /mbond/mbond.src /mc/mc.src, mcener.src /minmiz/egrad1.src, nraph.src /misc/hbuild.src, testch.src, xray.src /pert/block.src, epert.src, icfcnf.src, icpert.src, pert.src /tsme.src, tsms.src /quantum/qmset.src /util/prpref.src, sort.src /vibran/vibran.src, vibsub.src New Testcase: test/c30test/cmaptest.inp .............................................................................. 1.3.2 Analytic and grid-based Generalized Born Methods Three methods are available: (1) Grid-based methodology is a two parameter model which reproduces Poisson-Boltzmann solvation energies to within 1% accuracy. (2) Analytical method I is a 5-parameter model which reproduces absolute PB solvation energies to ~1.5% accuracy for any forcefield. (Only PARAM19/PARAM22/MSI22 have been tested.) Relative solvation energies are ok, but not much better than GBORN module for PARAM19. It is faster of the two analytical approaches. (3) Analytical method II is ~7 parameter model which reproduces absolute PB solvation energies to ~1% accuracy. Relative solvation energies are almost as good as grid-based method. Note that (A) All methods are intended to reproduce reentrant surface Poisson-Boltzmann solvation energies at 0.25 Angstrom grid spacing. (B) All parameters are largely forcefield independent, however tweaking them for other forcefields probably couldn't hurt. (C) Salt effects are available but not sufficiently tested. (D) See JCP paper Vol. 116, #24, 10606-10614 (2002) for details on Methods (1) and (2). Details of method 3) will be in upcoming J. Comp. Chem. article. (E) Also consult gbmv.doc and c29test/gbmv.inp. pref keyword: GBMV Files Added: source/energy/gbmv.src /fcm/gbmv.fcm Files Modified: install.com source/charmm/charmm_main.src, iniall.src /energy/energy.src, intere.src /util/prpref.src doc/developer.doc New Documentation: doc/gbmv.doc New Testcase: test/c30test/gbmv.inp ------------------------------------------------------------------------------ 1.4 Combined SCC-DFTB/CHARMM code for QM/MM Calculations Name : Qiang Cui, Marcus Elstner Email Address : cui@chem.wisc.edu, elstner@phys.upb.de Institution : Dept. of Chem. Univ. of Wisc. Madison Dept. of Theo. Phys. Univ. of Paderborn, Germany Date : July. 2002 An approximate density functional theory, the self-consistent-charge density functional tight binding (SCC-DFTB) method, has been implemented into CHARMM in a combined QM/MM framework. The method is as fast as the standard semi-empirical methods such as AM1 and PM3, with superior accuracy for many systems tested so far (especially hydrogen bonding interactions and reaction barriers). The current implementation has analytical first derivative and thus allows energy minimizations, reaction path search (e.g., travel) and molecular dynamics simulations; SCC-DFTB/MM also works with Monte Carlo. Replica can also be used, which makes it possible to use replica path and related approaches (such the nudged elastic band) for determining reaction path with the SCC-DFTB/MM potential; along the same line, path integral simulations can be carried out as well, although only for equilibrium properties at this stage. The parameter files for the SCC-DFTB atom types need to be obtained separately from Dr. M. Elstner (elstner@phys.upb.de). Files Added: source/sccdftbint/sccdftbini.src ---> interface code /sccdftbint/sccdftbsrc/ ---> scc-dftb source code /fcm/sccdftb.fcm ---> common block build/UNX/scctbint.mk ---> interface makefile /scctbt.mk ---> scc-dftb makefile Files Modified: install.com source/charmm/charmm_main.src, iniall.src /energy/energy.src /gener/update.src /mc/mcener.src /nbonds/nbexcl.src, nbonda.src, nbonds.src /quantum/addlnat.src /fcm/gamess.fcm New Documentation: doc/sccdftb.doc New Testcases: test/c30test/alanine_scc.inp ---> std. SCCDFTB/MM calculation /neb_scc.inp ---> Replica path with SCCDFTB /split_scc.inp ------------------------------------------------------------------------------ 1.5 NIH Developments Name : Xiongwu Wu and Bernard R. Brooks Email Address : brbrooks@helix.nih.gov Institution : National Institutes of Health Date : August 5, 2002 1.5.1 EMAP module for manipulate map objects The EMAP module is designed to manipulate map objects as well as interexchange between atomic objects and map objects. This module allow CHARMM to handle low resolution structural information in map format in molecular modeling studies. A core-weighted correlation function is implemented for map comparison. A grid-threading Monte Carlo method is implemented to search for the best fit of individual maps within a complex map. Files added: source/emap/emapop.src, emapsubs.src, emapio.c, emapdock.src /fcm/emap.fcm Files modified: source/charmm/charmm_main.src, iniall.src /io/mainio.src /util/prpref.src doc/commands.doc New Documentation: doc/emap.doc New Testcases: test/c30test/emap.inp /data/a7n.psf, a7n.crd .............................................................................. 1.5.2 Replica Path Code Enhancements Four working replica/path codes are merged. Files modified: source/energy/energy.src, epath.src /fcm/path.fcm .............................................................................. 1.5.3 Coordinate Manipulation Commands COOR TWIST command is added. COOR DUPLicate command is extended. Files modified: source/manip/corman.src .............................................................................. 1.5.4 Minimizer Enhancements NOEnergy function is added to STEEPD minimizer. Files modified: source/minmiz/steepd.src .............................................................................. 1.5.5 Standard Coding and Minor Enhancements Tailing black lines are removed as some compilers do not compile source files with extra lines. All variables must be decleared and fcm/impnon.fcm should be included at the beginning of each subroutine and function. Misplaced and/or misused ## keys are fixed. Minor enhancements are: (1) UNBUFIO() is called only for UNIX compilation (2) ROOMT(298.15D0) and ZEROC are moved to fcm/consta.fcm (3) Ability to move lonepairs added (4) Some dimensions increased: WDMAX=20 to 50 in miscom.src MAXPAR=256 to 512 in cmdpar.fcm (5) Marked comments in demands (6) SETMSI calls added Files fixed: source/cff/efscalar_cff.src, enbfast_cff.src, escalar_cff.src, parrdr_cff.src /charmm/charmm_main.src, iniall.src, miscom.src /correl/mantim.src /dynamc/dcntrl.src, dynamc.src, lonepair.src, nose.src, prssre.src /energy/ecnstr.src, genborn.src /fcm/cmdpar.fcm, consta.fcm, new_time.fcm, pbeq.fcm, reawri.fcm /flucq/fluqqmmm.src /gamint/blur.src /image/nbndgcm.src /machdep/machutil.src /manip/corman3.src /mbond/mbutil.src /minmiz/tnpack.src /misc/eef1.src, grid.src, surfac.src /nbonds/ace.src, ewald.src, nbndcc.src, pmeutil.src /pert/epert.src, tsmp.src, tsms.src /prate/charmmrate.src /quantum/qmleps.src, qmset.src /rxncor/rxndef.src /util/array.src, clcg.src, imsl.src