--------------------------------------------------------------------------- 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 c29b0 Developmental July 22, 2002 c29b1 Release August 15, 2002 CHARMM 30.0 c30a1 Developmental August 15, 2002 --------------------------------------------------------------------------- [0] About CHARMM29 Development As an on-going project, CHARMM development will be carried out with CHARMM version 29 series. The base revision is the beta release version c28b1. c29a1 is the first revision in the c29 developmental versions. The following describes new features and enhancements incorporated in the c29 development period. =========================================================================== [1] c29a1 Change Log The following are introduced and modified after the c28b1 release dated August 15, 2001. 1.1 Enhancements to the Monte Carlo and Dynamics modules Name : Aaron R. Dinner, Ioan Andricioaei, and Martin Karplus Email Address : aaron@bellatrix.pcl.ox.ac.uk Institution : University of Oxford Date : June 15, 2001 1) Volume scaling moves for constant pressure MC simulations were added. The method of choosing the volume changes and the acceptance criterion are those introduced by Eppenga and Frenkel (see mc.doc). Scaling can be applied BYATom, BYREsidue, or BYHEavy (the last maintains fixed hydrogen bond lengths). These modes of scaling can be mixed with the MOVE LINK command described below. The method works with images generated either by the CRYStal command (now officially supported for use with MC) or by a series of IMAGE TRANSformations (in which case the initial volume must be specified). 2) Dynamics restart files can now be written and read by MC, largely to make it easier to extend constant pressure simulations via storage of the CRYStal data structure. 3) A general MOVE LINKing facility was introduced to allow specification that certain MC moves always be performed together before applying the acceptance criterion. For example, one might wish to perform both a rigid body translation and a rigid body rotation of a solvent molecule in the same MC step; to do so, one would define each of these types of moves with MOVE ADD and then tie them to each other with MOVE LINK. At present, move instances within the move groups selected are matched by indices, so the move groups must have the same numbers of instances. Further details of the use of MOVE LINK are given in mc.doc. 4) Molecular dynamics simulations and Hybrid Monte Carlo simulations in the Tsallis (generalized) ensemble can now be performed. The modifications (which require the keyword TSALLIS to be included in pref.dat) involved a change to the calling sequence of DYNAMC. To invoke the Tsallis method in molecular dynamics, it is simply necessary to add to the DYNAmics command the keywords: TSALlis QTSAllis real EMIN real (see dynamc.doc). The Tsallis transformation is applied automatically in Hybrid Monte Carlo simulations if IACCept=2 (see mc.doc). 5) The path integral energy term is now supported by Monte Carlo. Small changes were made to the existing path integral setup routines (to create additional arrays for faster MC calculations, invoked by including the keyword MC on the PINT commandline) and to the existing path integral energy routine (to eliminate two unnecessary SQRT operations in the pairwise loop). In addition, an MC specific path integral energy routine (EPIMC) was introduced to pathint.src. At present, the allowed path integral moves are displacements of single beads (RTRN BYATom) or movements of five sequential beads such that the path integral spring lengths remain unchanged (CROT PIMC) (see replica.doc and mc.doc). 6) MC simulations with the semiempirical Mopac QM/MM terms are now supported. Files Added: source/mc/moveln.src (3) Files Modified: source/charmm/charmm_main.src (3) /charmm/iniall.src (1, 3) /dynamc/dcntrl.src (4) /dynamc/dynamc.src (4) /energy/pathint.src (5) /energy/polar.src (5) /energy/printe.src (1) /misc/pbeq2.src (5) /mc/armupt.src /mc/mc.src (1, 3, 4, 5) /mc/mcener.src (1, 5, 6) /mc/mcio.src (2) /mc/movead.src (1, 3, 5) /mc/moveio.src (1, 3, 5) /mc/mvcrot.src (5) /mc/mvdihe.src (5) /mc/mvhmc.src (4, 5) /mc/mvrtrn.src (1, 5) /fcm/mc.fcm (3, 5) /fcm/consta.fcm (5) /fcm/pathint.fcm (5) Modified Documentation: doc/dynamc.doc, mc.doc, replica.doc New Testcase: test/c29test/mctest03.inp, mctest04.inp, mctest05.inp, mctest06.inp /mctest07.inp ------------------------------------------------------------------------------ 1.2 The SASA Implicit Solvation Model Name : Urs Haberthuer and Amedeo Caflisch Email Address : atlantis@bioc.unizh.ch Institution : Biochemical Institute of the Universitiy of Zurich Date : July 28, 2001 The SASA model is a fast implicit solvation model suited for peptides. It is based on the solvent accessible surface area, using only two solvation parameters. It approximates this area with a simple analytical function that is easily derivable. It accounts for the screening effect of solute charges by using a distant dependent dielectric function and by neutralizing the charged groups of polar amino acids in exactly the same way as it is done in the EEF1 model. The SASA model has been successfully applied to peptides, removing the major artefacts of in vacuo simulations and even reproducing reversible folding. Latest benchmarks indicate that a simulation with SASA is only about 50% slower than an in vacuo simulation. Files Added: source/fcm/sasa.fcm /misc/sasene.src, sasini.src Files Modified: source/charmm/charmm_main.src, iniall.src /energy/energy.src, eutil.src, printe.src /fcm/energy.fcm New Documentation: doc/sasa.doc New Testcase: test/c29test/sasa.inp ============================================================================== [2] c29a2 Change Log The following are introduced and modified during the development period of August 15, 2001 through February 15, 2002. 2.1 TSRI Developments Name : Mike Crowley, Charles Brooks Email Address : crowley@scripps.edu, brooks@scripps.edu Institution : TSRI Date : December 27, 2001 (1) Added OPLS-AA protein force field to CHARMM. Pref keyword: OPLS Files modified: install.com source/charmm/iniall.src /energy/enefscal.src /util/prpref.src (2) Cray Binary File Read Modified traj read to permit reading Cray binary files on other machines. Pref keyword: T3ETRAJ Files modified: source/dynamc/dynio.src (3) Zero Length Message Changes to eliminate communication of zero length messages. Files modified: source/machdep/paral3.src, parset.src (4) Fixed IO control in solana Files modified: correl/solana.src (5) Code modifications for serial compile with RCFFT Pref keyword: RCFFT Files modified: install.com source/nbonds/pmeutil.src (6) Fixed ##If def logic. Files modified: source/mc/mcener.src, mvrtrn.src (7) Fixed/added selection logic to quick command. Pref keyword: QUICK_SELECT Files modified: install.com source/charmm/iniall.src /misc/quicka.src /util/prpref.src test/c29test/quicktst.inp [New] doc/miscom.doc (8) Changed pref keyword to unique identifier. Pref keyword: SASAE Files modified: install.com source/charmm/charmm_main.src, iniall.src /energy/energy.src, eutil.src, printe.src /fcm/energy.fcm /misc/sasene.src, sasini.src /util/prpref.src (9) Fixes for using slow and fast shake in same run, especially parallel. Switched indices on shake pair list from shkapr(n,2) to shkapr(2,n). Files modified: source/dynamc/dcntrl.src, mts.src /fcm/shake.fcm /gener/update.src /manip/corman.src, cshake.src, fsshake.src, shake.src (10) Added compile-code control to test cases. Files modified: test/c20test/hbuildst2.inp, imst2test.inp, rigidst2.inp, sbdtest2.inp /st2test.inp /c26test/block4.inp /c29test/sasa.inp ------------------------------------------------------------------------------ 2.2 Cornell University Developments Name : Nilesh Banavali, Wonpil Im, Benoit Roux Email Address : nilesh.banavali@cornell.edu, wonpil.im@cornell.edu, benoit.roux@med.cornell.edu Institution : Weill Medical College of Cornell University Date : December 27, 2001 (1) Enhancements of Extended Electrostatics, PERT, PBEQ and GSBP PBEQ and GSBP are updated and GSBP is implemented within PERT. Extended electrostatics has been made compatible with PERT. Substantial changes were needed in nbondg.src file to make EXTENDED ELEC compatible with PERT (storage of constant fields, etc...). Files Modified: source/fcm/pert.fcm /pert/pert.src, epert.src /nbonds/nbutil.src, nbondg.src, nbonds.src /misc/pbeq.src, gsbp.src, gsbp2.src (2) Branched IF Command The IF command is enhanced to handle IF-THEN-ELSE-ENDIF constructs. File Modified: source/charmm/miscom.src ------------------------------------------------------------------------------ 2.3 Updates of the SASA Implicit Solvation Model Name : Urs Haberthuer, Joannis Apostolakis and Philippe Ferrara Email Address : atlantis@bioc.unizh.ch Institution : Biochemical Institute of the Universitiy of Zurich Date : 26.12.2001 SASTRM has been moved from the CEPROP array to the CETERM array. Furthermore, the name to access to SASA mean solvation energy within the CHARMM input file has been changed from SASA to SASL in order to avoid confusion with the name used in the getpref() subroutine. The testcase now works fine. Flexibility for the user has been improved. The assignement of the SASA parameters is now based on the CHARMM atom types. Files Modified: source/energy/energy.src, eutil.src, printe.src /fcm/energy.fcm, sasa.fcm /misc/sasene.src, sasini.src doc/sasa.doc test/c29test/sasa.inp ------------------------------------------------------------------------------ 2.4 GAMESS-UK Interface Updated Name : Paul Sherwood Email Address : p.sherwood@daresbury.ac.uk Institution : CLRC Daresbury Lab. Date : January 16, 2002 Makefiles are updated for proper compilation with CHARMM. Documentation and testcase are also updated. Files modified: install.com build/UNX/Makefile_alpha, Makefile_alphamp, Makefile_gnu, Makefile_hpux, /Makefile_ibmrs, Makefile_ibmsp, Makefile_ibmsp3, Makefile_sgi, /Makefile_sun doc/flucq.doc, gamess-uk.doc source/flucq/fluqqmmm.src /fcm/gamess.fcm /gukint/gukini.src test/cquantumtest/alanine_guk.inp /data/alanine_guk.in ------------------------------------------------------------------------------ 2.5 Karolinska Institute Fixes and Enhancements Name : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : January 16, 2002 (1) A module for analysis of NMR dispersion relaxation to solvent is being added. File modified: source/correl/solana.src (2) Allow for, and test, the use of heap expansion on I8-pointer machines (alpha). The heap is still addressed using I4 integers. File modified: source/machdep/space.src (3) Check if images are present when PERT is invoked and warn user that the crystal/image facility has to be invoked AFTER pert. File modified: source/pert/pert.src (4) Document how to run parallel jobs under MPI-implementations not allowing rewind on stdin. File modified: doc/parallel.doc (5) In many testcases the test for parallel vs non-parallel execution is changed from if ?parallel .eq. 1 then stop to if ?NUMNODE .gt. 1 then stop so that testcases are run if an executable with parallel enabled is used on a single CPU. Files modified: test/c20test/constest.inp, enbtest.inp, hbuildst2.inp, ictest.inp /imst2test.inp, langtest1.inp, langtest2.inp, powelltes.inp /quasi.inp, rigidst2.inp, sbdtest2.inp, st2test.inp /vibpafl.inp, vibran.inp, vibrtst.inp, vibwat.inp /c22test/covaritst.inp, icfix.inp, icpert.inp, mewtest.inp /slowgr.inp, stdtest.inp, travel.inp, window.inp /c23test/nmrtest1.inp, nose1.inp, nose2.inp /c24test/block3.inp, dimb1.inp, dimb2.inp, pert2.inp, st1.inp /c25test/cwat.inp, ewald_grp.inp, ewald_pert.inp, fastest.inp /helix.inp, hrbestfit.inp, quiet.inp, rpath1.inp, vibwat25.inp /c26test/lambda_dynam.inp, luptst.inp, pathint.inp, tmc.inp, whamtest.inp /c27test/ace1.inp, adumb-enum.inp, adumb-phichi.inp, cubesgb.inp /gb_cff95_prot-test.inp, lnx_img.inp, testbycc1.inp /testbycc2.inp, testeef1.inp, testeef1imag.inp /c28test/gb_fep.inp, gb_ldm.inp, gb_mcmd.inp, gbmf19.inp, ldm_lang.inp /ldm_lang_slow.inp, ldm_rst.inp, ldm_rst2.inp, ldm_rst2_slow.inp /ldm_rst_slow.inp, mcmd_rst.inp, mcmd_rst2.inp, mcmd_rst2_slow.inp /mcmd_rst_slow.inp, pssp3.inp, replica_genborn1.inp /replica_genborn2.inp, replica_genborn3.inp /c29test/sasa.inp /ccfftest/cffdyn1.inp ------------------------------------------------------------------------------ 2.6 The SPASIBA Force Field Name : P. Lagant, G. Vergoten, R. Stote Email Address : rstote@chimie.u-strasbg.fr Institution : Universite Louis Pasteur, CNRS - ISIS Date : January 28, 2002 The SPASIBA force field is derived from spectroscopic studies. In the current implementation, the van der Waals and electrostatic interactions of the CHARMM force field are combined with the Urey-Bradley Shimanouchi terms for bond stretching, valence angle bending, torsional and improper torsional internal terms derived from spectroscopic data such as vibrational wavenumbers, dipole moments, rotation barriers for the SPASIBA force field. Files Added: source/gener/setup_spa.src /energy/ebaspas.src /fcm/spa_code.fcm, spacod.fcm, spapar.fcm Files Modified: source/charmm/iniall.src /io/coorio.src, parmio.src, psfres.src /gener/update.src /energy/ecnstr.src, ediff.src, eintern.src, energy.src, intere.src /manip/intcor2.src /image/eimage.src /fcm/dimens.fcm, psf.fcm, param.fcm, exfunc.fcm doc/energy.doc New Testcase: test/c29test/spasibatest.inp ------------------------------------------------------------------------------ 2.7 ACE2 - ACE Enhancements Name : Michael Schaefer Email Address : schaefer@piaf.u-strasbg.fr Institution : Universite Louis Pasteur, Strasbourg, France Date : Jan 30, 2002 ACE2 is an improved version of the ACE implicit solvent potential. It is designed to work for proteins of arbitrary size, as opposed to the original version of ACE which was limited to polypeptides of up to 15 residues. This is achieved by an improved treatment of the Born solvation radii. Currently, ACE2 appears to work quite reliably in conjunction with param19, but less so for all-atom parameters. Atom volumes are now read from file/stdin, and no longer from a volume table that is appended at the parameter file. Parameter files with new volumes (Schaefer et al., J. Comp. Chem. 22 (2001), 1857-1879) compatible with param19, par_all22_prot, par_all27_na are provided. The new ACE and ACE2 energy routine treats distances between atoms in the nonbonded exclusion list as invariant. The ACE energy of the new implementation does NOT reproduce the energy as calculated by the old (ACE1) implementation! Files Added: source/io/aceio.src toppar/acepar19.inp, acepar22_prot.inp, acepar27_na.inp Files Removed: source/nbonds/acean.src test/c27test/ace2.inp /data/param19-1.2.inp Files Modified: source/charmm/charmm_main.src, iniall.src /dynamc/dcntrl.src, dynlng.src, dynlngv.src /fcm/code.fcm, contrl.fcm, inbnd.fcm, param.fcm /gener/psfsum.src /io/mainio.src, parmio.src /manip/scalar.src /mc/mc.src, mvhmc.src /nbonds/ace.src, enbond.src, nbonds.src, nbutil.src /pert/block.src /util/selcta.src Modified Documentation: doc/ace.doc New/Modified Testcase: test/c27test/ace1.inp /c29test/ace_v2.inp, ace-adumb.inp /data/acepar19.inp Bugfixes: (1) ACE and ACE2 work properly when using BLOCK (including use of BLOCK while fixing atoms). (2) changed printout of SIGMA in nbutil, now given in cal/mol/A^2 i.e., a factor of 1000. bigger. (3) added IF statement in IESFIX to calculate fixed atom pair interaction only once for all nodes (parallel code). Known bugs: ACE2 distorts Trp sidechains ("butterfly") when minimizing with param19. ACE2 may lead to partial unfolding when performing a Langevin dynamics simulation of a protein with all-hydrogen parameters. The MC module is not expected to make use of the ACE2 enhancements. ------------------------------------------------------------------------------ 2.8 Bugfixes (1) MC with HMC moves and Tsallis weighting (IACCept 2) Name : Aaron R. Dinner Email Address : dinner@gold.cchem.berkeley.edu Institution : University of California, Berkeley Date : 17 January 2002 The Tsallis acceptance criterion applied to Hybrid Monte Carlo moves transforms the kinetic energy incorrectly. c29test/mctest05.inp checks this problem. DEKIN and DEPOT are passed separately to TSALLF via MCACPT (changing the calling sequences to both those routines). A flag (QHMC) is employed to force the correct operations in TSALLF. File fixed: source/mc/mc.src .............................................................................. (2) Velocity Verlet Restart Name : Arjan van der Vaart Email Address : arjan@schubert.u-strasbg.fr Institution : ISIS Date : November 8, 2001 Restart runs using the velocity Verlet integrator always give SHAKE errors, when heavy atoms bound to the SHAKE-able hydrogens are fixed. File fixed: source/dynamc/dynamvv.src .............................................................................. (3) Parallel EEF1 Fix Name : Arjan van der Vaart Email Address : arjan@schubert.u-strasbg.fr Institution : ISIS Date : December 5, 2001 The parallel implementation of EEF1 gives wrong solvation (and total) energies if more than one processor is used (forces are fine). (Note that the "dirty trick" comments have been deleted, since the "dirty trick" has been replaced by new code) File fixed: source/misc/eef1.src ============================================================================== [3] c29b0 Change Log The following are introduced and modified during the development period of April 15, 2002 through July 22, 2002. 3.1 Harvard Developments Name : Robert Petrella Email Address : petrella@tammy.harvard.edu Institution : Harvard University Date : July 02, 2002 (1) Poisson-Boltzman phi averages New commands allow calculation of averages of the electrical potential over the grid with or without an atom selection. Files Modified: source/charmm/iniall.src /misc/pbeq.src, pbeq2.src /fcm/pbeq.fcm doc/pbeq.doc (2) BYCC Non-bonded update Exclusion table is simplified. Files Modified: source/nbonds/nbndcc.src, nbonds.src, nbutil.src, nbexcl.src /fcm/exclar.fcm (3) Structural correlations in adaptive umbrella sampling New commands in adumb allow calculation of running averages for various structural variables as a function of the reaction coordinates of the system. Files Modified: source/adumb/cmds.src, umb.src /charmm/iniall.src /energy/energy.src /manip/intcor2.src /fcm/umb.fcm, umbcor.fcm doc/adumb.doc ------------------------------------------------------------------------------ 3.2 Analytical Second Derivatives of the EEF1 Potential Name : Ioan Andricioaei Email Address : andricio@tammy.harvard.edu Institution : Harvard University Date : 9 May 2002 The analytical expression of the second derivative matrix of the EEF1 potential term has been added in. The main code (i.e., the actual expression of the analytical second derivatives) was added in subroutine EEF1EN() of the misc/eef1.src code. The argument list of the EEF1EN() function has been modified. Three extra variables (last three in the argument list) are now passed: DD1, STACK(IUPT), and QSECD. In energy/energy.src, Robert Petrella's ATOMON, which was being pushed on the stack before, now is passed pushed on the heap. The other code that calls EEF1EN is in the additional three files listed below, and the EEF1EN() calls of each of them has been changed accordingly, i.e., by adding the three extra arguments. Files Modified: source/misc/eef1.src /energy/energy.src, intere.src /mc/mcener.src doc/eef1.doc New Testcase: test/c29test/eef1_2ndderiv.inp ------------------------------------------------------------------------------ 3.3 Bugfixes for the MC Module Name : Aaron R. Dinner Email Address : dinner@gold.cchem.berkeley.edu Institution : University of California, Berkeley Date : 17 June 2002 (1) MC uses its own routines to calculate the ACE energy term, and these were not updated with the recent change to the ACE energy term. The fix provides support for both the new ACE1 and ACE2. The testcase mctest06.inp was modified accordingly. (2) The algorithm for picking random displacements within a unit sphere was changed. The old algorithm gave a non-uniform distribution in volume (but did not violate detailed balance, so old simulation results are OK). This modification affects all RTRN type moves. (3) Some dynamically allocated arrays were not freed properly and now are. Several testcases were modified to test the memory usage. (4) Double-comma in one call of LNGFIL is fixed. Files involved: source/mc/mc.src (1, 2, 3 above) mcace.src (1, 2) mcener.src (1) movead.src (3) mvhmc.src (4) mvrtrn.src (3) test/c29test/mctest03.inp (2) mctest04.inp (3) mctest05.inp (3) mctest06.inp (1, 3) mctest07.inp (3) ------------------------------------------------------------------------------ 3.4 University of Minnesota Developments Name : Mireia Garcia-Viloca and Jiali Gao Email Address : garcia@chem.umn.edu Institution : U. of Minnesota Date : July 8, 2002 3.4.1 QM/MM(MOPAC) Enhancements (1) To allow qm/mm group-group interactions between mm-group and qm-molecule. In QM/MM calculations, charges are fully delocalized in the QM region, making it impossible to separate the QM region into groups. However, when a QM molecule is large, greater than a typical cutoff distance, it causes problems in nonbonded list generation and thus it is desirable to be able to separate the QM molecule into groups purely for the purpose of QM-MM nonbonded list. The optional keyword [GROUp] is appended to the QUANtum command to allow this operation. Note that the GROUp option is purely used for non-bonded list generation. Whenever an MM group interacts with any QM group, the MM group is included in the electronic structure calculation for the entire QM molecule, i.e., MM-group and QM-molecule interaction. Note that the default implementation of QM/MM nonbonded list allows for construction of the Fock matrix involving QM group - MM group interactions. This is avoided by specifying the new [GROUp] option. (2) Reorganization and implementation of the GHO parameters for AM1 and PM3 models. The GHO parameters for AM1 carbon are moved to qmdata file, and parameters for the PM3 GHO carbon have been developed and implemented. (3) Updating AM1 parameters for phosphorus, and PM3 parameters for carbon. MNDO parameters were used in the AM1 model for phosphorus in CHARMM previously. It is corrected in the distribution. Some GAUSSIAN parameters for carbon atom in the PM3 parameter set were missing in the initial distribution (c28b1) and they are corrected now. (4) Incorporation of a simple valence bond (SVB) term as a function of a raction coordinate in semiempirical QM/MM calculations. An empirical potential is added to the semiempirical QM/MM potential. The purpose of including this empirical potential is to correct energetic results from low level QM models in order to have good agreement with experimental or high-level ab initio results on activation energy and energy of reaction. The basis of this approach is to assume that the low level QM model can give a reasonable description of the shape and landscape of the potential energy surface for the problem that is being investigated. The form of the empirical potential function is a two state valence bond model and the new keyword in QUANtum [LEPS] is [SVB]. (5) Mulliken population analysis and averaging during a QM/MM MD simulation. A new optional keyword [CHDYn] is included in the QUANtum command to allow the calculation of average Mulliken population charges along a MD (QM/MM) trajectory. (6) Increase in dimension for EIGS and IFACT in subroutine MULIK2 (120 changed to MAXORB) to avoid array overflow. (7) Modifications in QM/MM decomposition analysis. A warning message is given when GHO atoms are used (not implemented). The velocity verlet integrator is now allowed for QM/MM energy decomposition. Files Modified: source/fcm/leps.fcm, quantm.fcm /quantum/qmdata.src, qmene.src, qmleps.src, qmset.src /dynamc/dynamc.src, dynamvv.src doc/qmmm.doc .............................................................................. 3.4.2 Potential of Mean Force Calculations and CHARMMRATE (1) To recenter a periodic system to the geometric center of the N first residues of the system (generally the protein-substrate complex) at each nonbonded list evaluation. Often it is desirable to keep the "active site" of a protein modeled by periodic boundary conditions near the center of the central unit cell. In combination with other facilities, one can avoid the image generation for periodic boundary systems. The keyword [CENT NCREs int] has been added as an optional command under DYNAmics operation. (2) To rearrange common blocks for biasing potentials in the rxncom.fcm and to change the format for umbrella sampling calculations. The array definition and location have been moved from the source file to a common block file. (3) Incorporation of a projection operator of the reaction coordinate in instantaneous normal mode analysis using the CHARMMRATE module. To remove the degree of freedom corresponding to the reaction coordinate from instantaneous normal mode analysis. The new keyword is [PMFZ] under the POLYrate command. (4) A one line modification of the install.com file for compilation of the crate (for charmmrate module) facility with CHARMM-POLYRATE interface. Files Modified: source/fcm/charmmrate.fcm, contrl.fcm, rxncom.fcm /prate/charmmrate.src /dynamc/dcntrl.src /nbonds/heurist.src /rxncor/rxndef.src, rxnene.src build/UNX/prate.mk doc/dynamc.doc, charmmrate.doc ------------------------------------------------------------------------------ 3.5 TSRI Developments Name : Scott Brozell, Mike Crowley and Charles L. Brooks, III Email Address : crowley@scripps.edu, brooks@scripps.edu Institution : TSRI Date : july 10 2002 (1) Faster image updates Files Modified: source/image/upimag.src (2) Speed enhancing tuning in REWALD aminly for sgi pref keyword: FASTEW Files Modified: source/charmm/iniall.src /nbonds/enbond.src, ewald.src /util/prpref.src (3) Faster communications for fft transpose (parallel) pref keyword: MPIFFT Files Modified: source/nbonds/pmeutil.src (4) Long Range vdW Continuum model with homogenenous density of atom types is used to compute the vdW correction to the energy for interactions beyond the cutoff. THe virial is also corrected. pref keyword: LRVDW Files Modified: install.com source/charmm/iniall.src /energy/energy.src, printe.src /fcm/deflts.fcm, energy.fcm, fast.fcm, inbnd.fcm /io/parmio.src /nbonds/nbexcl.src, nbutil.src /util/prpref.src doc/nbonds.doc, developer.doc New Testcase: test/c29test/lrvdw.inp (5) NOSKULL option added NOSKULL in pref.dat eliminates skull pref keyword: NOSKULL Files Modified: source/machdep/machutil.src (6) Bug fixes Files Modified: source/machdep/cstuff.src /manip/shake.src test/c29test/mctest03.inp, mctest04.inp ------------------------------------------------------------------------------ 3.6 Karolinska Institute Fixes and Enhancements Name : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : June 28, 2002 (1) The ECHO command A simplified command for text&data printing has been added. Similar to "write title" but simpler syntax. [ECHU integer | ECHU] ECHO ...... ECHO simply prints remainder of commandline, with standard substitutions, to OUTU or some other unit as specified by the ECHUnit command (if no unit number is given, printing will be to OUTU) Files Modified: source/charmm/iniall.src, miscom.src /fcm/stream.fcm doc/miscom.doc (2) New COOR ANAL options 2 New analysis options have been added to COOR ANAL: Analysis of magnetic relaxation dispersion from solute sites to water protons and Distance dependent Kirkwood factor (Hochtl et al JCP 109, 4927). Files Modified: source/correl/solana.src doc/corman.doc (3) Message Clarification The restart file written after an "ENERGY CHANGE TOLERANCE EXCEEDED" error is NOT a regular restart file. A message about this is now written to the output file. Files Modified: source/dynamc/dynamc.src (4) RMSD Matrix 2D-projection of the rmsd matrix computed in RMSDyn has been added (M.Levitt JMB 168, 621 (1983)). Output of the RMSD-matrix in matrix format has been added. Output from all the rmsd calculations is suppressed unless PRNLev is increased (This command should ideally access the trajectories through READCV; this however requires modifications to allow READCV to handle multiple trajetories, which I have not finished yet.) Files Modified: source/manip/rmsdyn.src /util/imsl.src (error output from zxmin has been suppressed) doc/dynamc.doc, subst.doc test/c29test/rmsdyn.inp (New) (5) COOR DMAT Clarification COOR DMAT output in either the old "full" format or the matrix-elements only has been cleanly separated. An option to write out a matrix with a "1" as the element when a contact is present, and "0" otherwise, has been added. This is useful when the matrix is to be used as a projection matrix later on. Files Modified source/manip/corman2.src doc/corman.doc (6) PERT Variables Three new CHARMM variables with results from PERT-runs have been added Files Modified source/pert/pert.src doc/subst.doc (7) I/O Control I/O statements in MMFP have been protected for parallel runs (IF(PRNLEV.GE.2)) Files Modified source/misc/mmfp.src (8) Mass Unit Correction Units for the "mass" of the extended system thermal piston have been corrected in pressure.doc Files Modified doc/pressure.doc ------------------------------------------------------------------------------ 3.7 NIH Developments Names : Milan Hodoscek, Lee Woodcock, Paul Sherwood, Bernie Brooks Email Address : milan@cmm.ki.si Institution : National Institutes of Health Date : July 9, 2002 3.7.1 QM/MM extension of REPLICA/PATH and similar methods We extended the functinality of the REPLICA/PATH like methods to enable running them with the QM/MM potential. All the functionality of the RPATH command is implemented. The method uses parallel/parallel setup. Files Modified: source/cadint/cadini.src /dynamc/dynamcv.src /fcm/gamess.fcm, parallel.fcm /flucq/flucq.src, fluqqmmm.src /gamini/ddi.src /gener/update.src /gukint/gukini.src /machdep/paral1.src, paral2.src, paral3.src, parset.src /nbonds/nbonda.src, nbonds.src /quantum/qmset.src doc/replica.doc .............................................................................. 3.7.2 Merging of GAMESS, GAMESS-UK, and DIESEL interfaces into a single file The interfaces to the programs GAMESS, GAMESS-UK, and DIESEL were merged. Files Modified: source/gukint/gukini.src /charmm/charmm_main.src /energy/energy.src /fcm/gamess.fcm doc/gamess.doc build/UNX/gmscomp New files: doc/diesel.doc Files Deleted: source/gamint/gamini.src ------------------------------------------------------------------------------ 3.8 GAMESS-UK Interface Updated Name : Paul Sherwood Email Address : p.sherwood@daresbury.ac.uk Institution : CLRC Daresbury Lab. Date : July 12, 2002 3.8.1 INTEGER8 pref.dat keyword This provides a generic way to switch to 64 bit integers, it is a generalisation of the code provided for GNUALPHA by Ben Webb with a few additional changes that were found to be necessary. It has been tested together with the sgi64 and alpha targets it should also work with gnu/cfort (the original GNUALPHA platform) Files Modified: install.com source/machdep/paral1.src, paral2.src, paral3.src, startup.src, cstuff.src build/UNX/Makefile_alpha, Makefile_sgi64 .............................................................................. 3.8.2 Other GAMESS-UK Interfacing changes Added tests on GAMESSUK pref.dat keyword to remove BLAS code when linked to GAMESS-UK (will be provided either by GAMESS-UK itself or by libraries it will use). File Modified: source/util/array.src /gukint/gukini.src ------------------------------------------------------------------------------ 3.9 Bugfixes and Enhancements (1) National Institutes of Chemistry (Slovenia) Bugfixes Name : Milan Hodoscek Email Address : milan@cmm.ki.si Institution : National Institute of Chemistry, Ljubljana, Slovenia Date : July 9, 2002 (1.1) Compilation on HP, and others Missing stream.fcm for prnlev variable (HP didn't compile) in efscalar_cff.fcm, missing comma in format statement. Files involved: source/cff/efscalar_cff.src /pert/block.src .............................................................................. (1.2) Write the trajectory file in the ASCII double precision formart This enhancement is needed for easier analysis of integration algorithms and others. Files modified: source/charmm/iniall.src /dynamc/dcntrl.src, dynio.src /fcm/reawri.fcm /minmiz/minmiz.src .............................................................................. (1.3) MD-GRAPE-II modifications MD-GRAPE-II support was extended for ewald method. Files involved: source/nbonds/grape.src /nbonds/nbutil.src /dynamc/dynamc.src .............................................................................. (1.4) Support for general exponent in the HQBM method The HQBM method was enhanced to support any exponent. Files involved: source/energy/hqbm.src /fcm/hqbm.fcm doc/hqbm.doc .............................................................................. (1.5) LARGE XXLARGE dimensions generalized The dimens.fcm was fixed to support LARGE and XXLARGE Files involved: source/fcm/dimens.fcm .............................................................................. (1.6) PBEQ fix: allows Epsilon other than one with the forces Allows Epsilon other than one with the forces Files involved: source/misc/pbeq2.src .............................................................................. (1.7) Subroutine name conflict with GAMESS Subroutines DIVIDE and FACT have the same names as in the GAMESS program Files involved: source/nbonds/fma.src /util/calc.src .............................................................................. (2) Installation of a SUN MPI version Name : Roland H. Stote Email Address : rstote@chimie.u-strasbg.fr Institution : Universite Louis Pasteur, CNRS - ISIS Date : June 18, 2002 A SUN MPI port is added. install.com is modified to set up a separate subdirectory for a SUN MPI version of CHARMM. The options used in Makefile_summpi are valid as well for SUN monoprocessor. Files involved: install.com build/UNX/Makefile_sunmpi (New) .............................................................................. (3) TSM bugfix Name : Robert Petrella Email Address : petrella@tammy.harvard.edu Institution : Harvard University Date : July 02, 2002 Format I is fixed to I4. File Fixed: source/pert/tsms.src .............................................................................. (4) Array Declared for the Grid Code Name : Aaron R. Dinner Email Address : dinner@gold.cchem.berkeley.edu Institution : University of California, Berkeley Date : 17 June 2002 GridRadii is a local array but declared adjustable size in GridEnergy. The bug prevents compilation on at least the Portland Group compilers. The GridRadii array was not used by GridEnergy and was deleted. File Fixed: source/misc/grid.src .............................................................................. (5) SHAKE Compile Name : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : June 28, 2002 nconst and nconst_tot were defined twice in one routine. Subroutine fill_fstprs seems to require MPI communications: added protection by ##IF MPI File Fixed: source/manip/shake.src .............................................................................. (6) NULL String Name : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : June 28, 2002 Replaced no-good null string ('') in subroutine calls. This affects the testcase output of c29test/sasa.inp.2 File Fixed: source/misc/sasini.src .............................................................................. (7) PBEQ Probe Size Name : Benoit Roux Email Address : Benoit.Roux@med.cornell.edu Institution : Weill Medical College of Cornell University Date : July 4th 2002 If the user is requesting a re-entrant calculation of the solvent- accessible surface area of the protein, then the water probe should be 1.4 angtroms. Otherwise the result is not meaningful. Therefore, we modified the setup for the default values so that a probe size of zero is used, unless a re-entrant calculation is requested. More information about this is also printed out to warn the user. File Fixed: source/misc/pbeq.src ============================================================================== [4] c29b1 Change Log Some features are still under development and are determined not to be included in the forthcoming beta releases of CHARMM 29 at the CHARMM meeting (Harvard University, July 12-13, 2002). The c29b1 release of August 15, 2002 is prepared with the following functions removed. 4.1 The SPASIBA Force Field Removed Files Removed: source/gener/setup_spa.src /energy/ebaspas.src /fcm/spa_code.fcm, spacod.fcm, spapar.fcm test/c29test/spasibatest.inp Files Modified: source/charmm/iniall.src /io/coorio.src, parmio.src, psfres.src /gener/update.src /energy/ecnstr.src, ediff.src, eintern.src, energy.src, intere.src /manip/intcor2.src /image/eimage.src /fcm/dimens.fcm, psf.fcm, param.fcm, exfunc.fcm doc/energy.doc ------------------------------------------------------------------------------ 4.2 GBMF, GBMV, and CMAP codes Following the request of the original developer of TSRI, the GBMF code is removed and is replaced by the GBMV code. The TSRI check-in was integrated into c29b0 as a whole and GBMF, GBMV and CMAP codes are removed for c29b1. GBMV and CMAP will be further developed in c30. Files removed: source/energy/gbmv.src /fcm/gbmv.fcm test/c28test/gbmf19.inp Files Modified (GBMF/GBMV): install.com source/charmm/charmm_main.src, iniall.src /energy/energy.src, genborn.src, intere.src /fcm/genborn.fcm /io/psfres.src /util/prpref.src doc/developer.doc Files Modified (CMAP): 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 ------------------------------------------------------------------------------ 4.3 Structural Overlap Code Remvoed Structural overlap method by using Gaussian overlap integrals was integrated into c29b0 with Milan's other check-in and is removed for c29b1. The OVERLAP code will be developed in c30. Files Removed: source/misc/olap.src /energy/eolap.src /fcm/olap.src Files Modified: source/charmm/charmm_main.src, iniall.src /energy/energy.src, eutil.src, printe.src /fcm/energy.fcm /util/prpref.src