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CHARMM Developer’s Change Log

Entries in each node are recorded by CHARMM developers to indicate new and modified features of CHARMM during the development cycle, i.e., the alpha version period.

------------------------------------------------------
 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
      c22g3    Release           November   3, 1992
      c22g4    Release           March      1, 1993
      c22g5    Release           August     1, 1993

 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

 CHARMM24.0
      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
------------------------------------------------------

Summary of Modifications of Developmental CHARMM21 to CHARMM22

  • Linear pressure ramping added to CPT code (see Other Points)

  • Frequency based crystal update is now supported

  • Relevent new keyword is IXTFrq (see image)

  • Constant Pressure and Temperature (CPT) dynamics (See Other Points)

    • TRICLINIC unit cell is now supported.
  • Miscellaneous commands:

  • Minimization: new keyword (FMEM) for ABNER minimizer (see Energy Manipulations: Minimization and Dynamics)

  • Internal coordinates (see The Internal Coordinate Manipulation Commands)

    • New commands:
      • IC SAVE
      • IC RESTore
      • IC RANDom [iseed]
    • Internal coordinates converted to double precision.
  • Coordinate Manipulation (See Miscellaneous Commands and CORMAN.DOC)

    • New inline command varaibles added: ?theta, ?xmove, ?ymove, ?zmove, ?rms
    • New CORMAN commands added:
      • COOR HELIx
      • COOR PUCKer
      • COOR COVAraince
      • COOR SEARch ... RBUFF ...
  • Energy, Angles

    • Urey-Bradley 1-3 terms have been added as an option.
    • Format of parameter file affected. (See Input-Output Commands)
    • Energy analysis code added (ANALysis ON command). (See Analysis Commands)
  • NOE distance restraints (See CONSTRAINTS)

    • Overhaulled to become a general distance restraint term.
    • Commands syntax overhaulled as well.
  • PSF common structure modified

    • Unused PSF arrays removed. All size limits increased.
    • Binary file format changed to INTEGER*4 and REAL*8
    • PSF numbers added to ?variable list (See Miscellaneous Commands).
  • Output redirecting implemented. (See Miscellaneous Commands)

    • OUTU replaces all writes to unit 6.
  • ATLIM modified to allow a limit of several days.

  • Free energy perturbation commands added. (See Free Energy Perturbation Calculations)

    • Several new commands and features have been modified to allow free energy perturbation simulations to be performed.
  • Partition function and classical free energy codee added to the vibrational analysis code. (See Vibration Analysis)

    • Atom selection added for EDIT commands.
    • Atom selection added for WRITE SECOnd-derivatives CARD command.
  • New time series commands and options (See Correlation Functions)

    ENTER PUCKer
    ENTER HELIx
    ENTER RMS
    ENTER ENERgy
    ENTER RMS [MASS] atom-selection
    ENTER ATOM CROSsproduct
    ENTER FLUC CROSsproduct
    ENTER VECT CROSsproduct
    ENTER HBOND
    ENTER MODE
    ENTER RMS [MASS] [ORIEnt]
          ...
    TRAJ ... atom-selection
    MANTIME SQUARE (vectors now allowed)
    MANTIME ABS    (vectors now allowed)
    MANTIME ACOS
  • Off-by-one error removed in time series data (time series now do not start at time zero, but at time DELTA*SKIP).

  • Langevin dynamics modified.

    • An improved algorithm has been incorporated which gives a more accurate integration at low gamma values as well as the proper brownian dynamics limiting values in the large gamma limit (and is more efficient).
    • The gaussian random generator has been replaced to give a much more accurate distribution and uses only one random number call per atom by using an error function lookup table.
  • Miscellaneous commands added. (See Miscellaneous Commands)

    • DIVIde, EXONent, RANDom, and SHOW
  • New miscellaneous variables added.

    • ?rand
  • Precision and index limits improved.

    • The entire program (except for the graphics section) has been converted to REAL*8 and INTEGER*4 from REAL*4 and INTEGER*2.
  • Constant Pressure and Temperature (CPT) dynamics added. (See Other Points)

    • Pressure analysis code added.
    • NTRFRQ usage modified so that it works for IMAGES and CRYSTAL.
  • Heuristic nonbond update feature added. (See Generation of Non-bonded Interactions)

  • New (consistent) energy print format with search line indicators.

  • Graphics subsection added for workstations.

  • New GRADient option added for most minimization methods for searching for saddle points.

  • FAST option is now the default. It is no longer necessary to have the command “FAST 1” in order to use the efficient energy routines.

  • Constrained reference now only set for selected atoms for the CONS HARMonic command (the old method limited versatility). (See CONSTRAINTS)

  • Parallelization for shared memory multi-processor machines has been implemented. Functionality for the fast energy routines has been increased. The vector/parallel routines will now to no electrostatics and novdw as well as simple cut-offs.

  • SPECIfy command. Controls various options such as I/O buffer flushing maximum number of processors to be used and whether to use the fast nonbond list generator.

  • SYSTem "unix bourne shell commands" This command permits the user to issue Unix shell commands from the program. The command string must be enclosed in double quotes to prevent the CHARMm parser from converting the string to uppercase.

  • SHAKE FAST This command specifies the use of the new vector/parallel SHAKE

  • Deleted Features:

    • The old VAX analysis facility has been removed.
    • Sigma van der Waal switching and shifting options has been removed.
    • BARRI command removed.

Major Enhancements and Developments in CHARMM22

As CHARMM20 is not clearly defined, it is not straightforward to sort out major differences between the current version of CHARMM (CHARMM22.0) and a previous version (CHARMM20 or CHARMm21). The VAX version CHARMM on HUCHE1 turns out to be a “developmental” version towards CHARMM21 and contains the crystal facility, BLOCK, etc. The following is prepared by comparing the developmental VAX version CHARMM21 source code and that of CHARMM22.0.

Obsolete Modules Deleted from CHARMM20

  1. GRAMPS It is supported only in the VAX version CHARMM20. TH:[MK.PROT.SOURCE.VAX]GRAMPS.FLX contains an interactive routine that writes several files for the command language interpreter for producing computer graphics on the Evans & Sutherland Multi-Picture-System called GRAMPS. This obsolete feature is no longer supported in CHARMM22.
  2. PARAmeter Optimization PARMOP is not incorporated in the VAX version CHARMM20 either except at the point of command parsing. It seems that the feature has never been included in the central version.

New Features in CHARMM22

  1. BLOCK

    The developmental CHARMM21 VAX version supports some BLOCK commands. The BLOCK commands are used to partition the molecular system into blocks and allows for the use of coefficients that scale the interaction energies between the blocks. Specific commands to carry out free energy simulations with a component analysis scheme have been implemented.

  2. CRYStal

    The CRYStal commands are used to build a crystal with any space group symmetry, to optimize its lattice parameters and molecular coordinates and to carry out a vibrational analysis. The CRYSTAL program is incorporated into the IMAGE module. The VAX developmental version has a separate CRYSTL module.

  3. COOR COVAri

    The new COORdinate subcommand COVAriance is added. It computes covariances of the spatial atom displacements of a dynamics trajectory for selected pairs of atoms.

  4. CORR HELIx / CORR PUCKer

    The New CORRelation commands HELIx and PUCKer are introduced. The HELIx command computes time series of the helical axis orientation and PUCKer computes that of the sugar pucker phase and amplitude.

  5. DRAW, GRAP

    The new module GRAPHICS provides CHARMM the capability of displaying molecular structures when run on a graphics workstation. (Currently works only on Apollo machines.)

  6. HBTRim

    The HBTRim command deletes hydrogen bonds that have an energy of interaction that is higher than the specified cutoff. This command is used to reduce a list of hydrogen bonds to that of important hydrogen bonds.

  7. MOLVIB

    MOLVIB is a general purpose vibrational analysis program, suitable for small to medium sized molecules (less than 50 atoms). It performs canonic force field calculations (KANO), crystal normal mode analysis for k=0 (CRYS) and other vibrational analyses in internal coordinates or in Cartesian coordinates. Details are documented in The MOLVIB Module of CHARMM.

  8. PERT

    The PERTurbe command allows the scaling between PSFs for use in energy analysis, comparisons, slow growth free energy simulations, and widowing free energy simulations. This is a rather flexible implementation of free energy perturbation that allows connectivity to change. Also, three energy restraint terms (harmonic, dihedral and NOE) are subject to change which allows a flexible way in which to compute free energy differences between different conformations.

  9. QUANTUM

    Quantum mechanical and molecular mechanical combined force field method is implemented by employing the semi-empirical SCF method of the MOPAC program. This module has not been tested nor documented. The code does not confirm CHARMM coding standards. The future of the code is not certain at the time of the current release.

  10. RMSD

    The new RMSDyn routine is a modified CORMAN routine by William D. Laidig, which computes the RMS difference between two trajectory files and make a matrix of results.

  11. RXNCOR

    The RXNCor command is used for defining a reaction coordinate for any molecule based on its structure and impose an umbrella potential along that reaction coordinate (i.e., to run activated dynamics along this coordinate) in order to trace out the free energy profile during the structural change along the coordinate.

  12. SOLANA

    The solvent analysis facility computes solvent averaged properties, e.g., the solvent velocity autocorrelation function, mean-square displacement function, solvent-solvent radial distribution functions, solvent-reference site radial distribution function, and the solvent - reference site deformable boundary force.

  13. TRAJ

    The new TRAJectory command is used to merges or to break up a dynamics coordinate or velocity trajectory into different numbers of units.

  14. TSM

    The Thermodynamics Simulation Method module performs the free energy simulation.

  15. Urey-Bradley Energy Term

    Urey-Bradley 1-3 terms have been added. The developmental CHARMM21 also includes U-B terms.

  16. Update

    Two new non-bonded neighbour list updating schemes are introduced; one has something to do with an automated updating procedure and the other with the list generation algorithm.

    When INBFRQ is set to -1 (which is the default), heuristic testing is performed every time ENERGY is called and a list update is done if necessary.

    A new routine NBNDGC (nbndgc.src), a modification of NBONDG, is introduced. NBNDGC is based on a cubical grid searching algorithm and generates the nonbonded list in linear time, as opposed to quadratic. On the Convex C220, which is a vector machine, it is faster than NBONDG for any system larger than a few hundred atoms.

  17. Integrator

    The leap-frog integrator has been implemented. While the “old” Verlet integrator is still available via the DYNA VERLet command (and is the default), the new integrator can be accessed by DYNA LEAP. The velocity Verlet integrator is also added in CHARMM. This new velocity Verlet integrator can be called by DYNA VVER.

  18. Constant Pressure & Temperature Dynamics (DYNCPT)

    The constant pressure/temperature dynamics algorithm is implemented following the paper by Berendsen et al. (J. Chem. Phys. (1984) 81(8) p.3684).

Modification of CHARMM20 to CHARMM22

  1. ANALysis

    The VAX version analysis facility is replaced by an energy contribution array (ECONT). All evaluated energy terms are partitioned into each atomic contribution and collected in the array, which is accessible through the SCALAR command.

  2. XRAY

    The XRAY command of CHARMM20 is replaced by the READ XRAY command in CHARMM22. In CHARMM22, all I/O functions are parsed in mainio.src. The subroutine XRAY is changed to RDXRAY, which generates a card file compatible with Richard Feldmann’s XRAY display program.

  3. NOE

    NOE constraint has been overhauled. It now handles general distance restraint terms.

  4. MISCOM

    The miscellaneous command parser (miscom.src in CHARMM22) is modified.

    1. The SKIPE command is parsed in MISCOM.
    2. New command parameter (@x) handling commands are added: DIVIde, EXPOnentiate, GET, MULTiply and SHOW.
    3. The RANDOM command is added to set random number specifications.
    4. The STOP command is parsed in MISCOM.
    5. The QUICk (or Q) command is added to carry out a quick coordinate analysis.
  5. HANDLE

    The subroutine HANDLE is improved to accept command line arguments given with the CHARMM command issued to an operating system. It works on most UNIX, UNICOS and VAX/VMS versions.

  6. Command Parameters

    In CHARMM20, we have ten command parameters @n, where n is a single digit, 0 through 9. It is expanded to support any single alpha-numeric character so that one can use upto 36 command parameters (0-9, a-z).

  7. Dynamic Memory Allocation

    Most of UNIX versions now support VEHEAP. VEHEAP was originally implemented by employing VAX/VMS system calls. It expands the HEAP common block when more HEAP space is needed. In UNIX versions, we use the UNIX system library routine malloc(), if available (the availability depends on the machine), to perform the same function.

  8. File Format / Compatibility

    All binary files except dynamics trajectory are written in double precision format and not compatible with old versions. For PSF, topology, parameter, etc. one should use CARD format to transfer previous version files to CHARMM22. Trajectory files are written in single precision and compatible with all CHARMM versions and QUANTA. Old version dynamics restart files are not compatible with CHARMM22.

  9. Random Number Generator

    All random number routines are implemented in double precision (64-bit words). Box-Muller algorithm is used for generating a Gaussian random deviat. A machine specific random number routine (RANV of CONVEX VECLIB) is used in a CMU version.

Major Enhancements and Developments in CHARMM23

As an on-going project, CHARMM development has been carried out with CHARMM version 23 series. CHARMM development entails two objectives. First, we maintain an integrated macromolecular science package running on a wide range of computing devices. Second, we incorporate and exploit molecular simulation methodologies at the frontier of current research.

In order to establish the first objective, we maintain all source and support files under CVS (Concurrent Versions System) control. The ROOT repository is tammy.harvard.edu:/prog/chmgr/CVS. CHARMM23 is stored in /prog/chmgr/CVS/c23a. A particular version is retrieved with the version name as the rivision tag (e.g., c23f3).

Since we branched out from the CHARMM22 release version c22g2, we have made two alpha versions and four FORTRAN versions.

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

c23f3 is the current release version. As the “f” in c23f stands for FORTRAN version, we converted FLECS source into FORTRAN. The conversion task had been completed as of c23f2. Now CHARMM is written in full FORTRAN except several machine dependant codes written in C. The universal languages (C and FORTRAN) make it easier to port to new machines in a broad range of architectural designs and to incorporate new methodologies into a research version of CHARMM.

During the c23 development cycle, we have added and tested several new features as described below. We have also ported c23 to new machines and supported c23f versions on the following platforms.

Platforms Supported

RREFX key Platforms
ALLIANT Alliant
ALPHA DEC alpha workstation
APOLLO HP-Apollo, both AEGIS and UNIX
ARDENT Stardent
CONVEX Convex Computer
CRAY Cray Research Inc.
DEC DEC ULTRIX
HPUX Hewlett-Packard series 700
IBM IBM-3090 running AIX
IBMMVS IBM’s MVS platform
IBMRS IBM RS/6000
IBMVM IBM’s VM platform
IRIS Silicon Graphics
MACINTOSH Apple Macintosh computers (system 7)
SUN Sun Microsystems
VAX Digital Equipment Corp. VAX VMS

New Features in CHARMM23

  1. Cray Fast Code (Douglas J. Tobias)

    Vector/parallel code for energy calculation, shake, and nonbonded list generation on the Cray was implemented. Dynamic heap and stack allocation on the Cray was added.

  2. PARALLEL (Bernard R. Brooks)

    General code for support of CHARMM on MIMD machines is completed. This includes control of the I/O levels for all file I/O. For parallel machines or workstation clusters, only node zero performs I/O and it broadcasts are to other nodes.

    All compuationally intensive code exercised in MD is now fully parallel which includes: DYNAMC, ENERGY (and most subsections), SHAKE, PRSSRE, DYNLNG, IMAGES,... Almost all comutationally intensive code in the first order minimizers is fully parallel. Other usage of the energy routines are parallel (such as the energy time series in CORREL).

  3. Dynamics Integrator

    1. Leap-Frog Integrator (Bernard R. Brooks)

      Berendsen’s method was modified so that it would work for very small systems and for very weak coupling constants. Now it is possible to use SHAKE with CPT and get correct pressures and temperatures. Another change is to calculate the change in potential energy due to the constant pressure algorithm. The energy lost due to the changes in box size is now added to the kinetic energy during the constant temperature procedure. This allows the constant presure code to nearly conserve energy and allows the constant temperature code to be used with weak coupling times. This correction was made when we found that water box simulations with the Berendsen’s method were running about 10 degrees too cold when both temperature and pressure coupling times of 1ps were used. Now the correct target temperature is achieved, even in the limit of very weak couplings.

    2. EULER Dynamics Integrator (Bernard R. Brooks)

      The incorporation of of the Langevin/Implicit Euler dynamics integrator has been achieved. The effect is to remove the energy in the high frequency degrees of freedom which eliminates the noise in free energy studies where bonds are being modified. To support the Implicit Euler integration, a Truncated Newton Minimizer has been added. This minimizer may be used directly using the MINI TN command. The minimizer is not yet fully implemented (it works, but is not as efficient as it will be), but it is already very competitive relative to existing minimization methods. MINI TN does not work with SHAKE. This code has been developed by Tamar Schlick at NYU. It has been integrated within CHARMM with some modifications.

    3. EHFC: High Freequency Correction (Bernard R. Brooks)

      The leap-frog dynamics integrator has been modified to have an improved high frequency correction (HFC) term. With the old term, energy was conserved within a harmonic degree of freedom, but total energy would drift as energy exchanged between high and low frequency degrees of freedom. The new code avoids this problem. The total energy and kinetic energy that is printed in the first line of dynamics energy printout has reverted to the standard Verlet energies, and these match the output of the old integrator. The HFC terms (total energy, and kinetic energy) are now printed on the second line. The fluctuation of the HFC total energy is usually an order of magnitude smaller than that of the total energy. The HCF total energy is a good indicator of problems with NVE dynamics because small changes in total energy are not lost in the noise of high frequency oscillations.

    4. Velocity Verlet Integrator (Masa Watanabe)

      Velocity Verlet method has been implemented. Two integrator (Verlet and Leap-frog) methods presented in CHARMM have their own flavors, but Verlet method handles velocities rather awkward and may introduce some numerical imprecision. On the other hand, the Leap-frog integrator minimizes loss of precision on a computer, but it does not handle the velocities in a satisfactory manner. Velocity Verlet integrator can store positions, velocities, and accelerations all at the same time and minimizes round-off error.

    5. Nose-Hoover Constant Temperature Method (Masa Watanabe)

      The constant temperature method has been implemented based on S. Nose, JCP 81, 511 (1984) and W.G. Hoover, Phy. Rev. A 31, 1695 (1985). This is an another type of constant temperature method, but an equilibration time in the vicinity of the desired temperature is faster than other routines which are available in CHARMM. Also multi-temperature controls are also developed in order to equilibrate the system faster and keep the system in the desired temperature well. This method works with Verlet and Velocity Verlet integrators.

    6. Multiple Time-Scaled Method (Masa Watanabe)

      Tuckerman et al proposed a reversible RESPA algorithm recently (Tuckerman, Berne, Martyna, JCP 97, 1990 (1992)). Previous MTS methods have the disadvantages of loosing accuracy due to the approximation of holding the slow variables fixed while integrating the equations for the fast variables. But in this reversible RESPA equations of motions are derived from Liouville operators and Trotter theorem. The method gives more accurate dynamics than previous methods. In this implementation, one can specify up to three different time steps in dynamic simulation run.

  4. RISM (Reference Interaction Site Model) (Georgios Archontis)

    The RISM module allows the user to calculate the site-site radial distribution functions g(r) and pair correlation functions c(r) for a multi-component molecular liquid. These functions can then be used to determine quantities such as the potential of mean force or the cavity interaction term between two solute molecules into a solvent, and the excess chemical potential of solvation of a solute into a solvent. The change in the solvent g(r) upon solvation can be determined and this allows for the decomposition of the excess chemical potential into the energy and entropy of solvation.

  5. MMFP (Miscellaneous Mean Field Potential) (Benoit Roux)

    The MMFP Commands are primarily used for setting up special restraining potentials on some or all of the atoms. The key word MMFP is used to enter the MMFP environement. In the MMFP environment, all miscellaneous commands (label, goto, if, etc...), and string substitutions (with @1, @2, etc...) are supported. The key word END returns to the main parser. The restraining potentials are used in all energy calculations, unless SKIP is used. The subcommand RESET clears the potential. This module is still under development and only the subcommand GEO is released. The subcommand GEO (standing for geometrical) is used to setup various restraining potential (spherical, planar or cylindrical restraints) on some or all atoms. The selection specification should be at the end of the command. The default atom selection includes all atoms. Future subcommands will include continuum electrostatic reaction field and solvent mean field potentials. Expected date of release is Spring 1994.

  6. NMR Analysis (Benoit Roux)

    The NMR commands may be used to obtain a set of time series for a number of NMR properties from a trajectory. Among the possible properties are relaxation rates due to dipole-dipole fluctuations (T1, T2, NOE, ROE), chemical shift anisotropy and Deuterium order parameters for oriented samples.

  7. REPLICA (Leo Caves)

    Tool to support LES and MCSS calculations. Performs replication of arbitrary regions of PSF. Data structure interfaces to non-bond list generation routines, to perform appropriate exclusions. In association with BLOCK can provide appropriate energy/force normalizations for various classes of methods employing replicas.

    Introduced REPLICA and REPDEB preprocessor directives. Code for cray multi-tasking list generation routine used inference and has not been tested. Convex parallel code works fine. Added miscellaneous parameters to report number of atom/group pairs from non-bonded routines: ?NNBA, ?NNBG, ?NNBI for atom/group/images respectively. For replica-based exclusions from the list there are ?NRXA and ?NRXG for atom and group exclusions.

  8. Clustr code integrated into CORREL (Charles L. Brooks III)

    The CLUSTER command clusters time series data obtained within the CORREL facility. The data are grouped into sets with similar time series values, using euclidean distance as the dissimilarity measure between different time frames of a set of time series. It is useful, for example, for grouping together similar conformations or energy levels.

  9. GRAPHICS (Richard M. Venable)

    Graphics code converted to FORTRAN and overhauled. Versions that work with Xwindows and GL are in progress. A new preflx keyword, NODISPLAY, builds a version which produces HPGL, PLUTO FDAT, and LIGHT.atm files without requiring any screen display capabilities. The SG (IRIS) code incorporation is relatively untested. Postscript file output similar to HPGL (but much nicer looking, hopefully) is also implemented.

Major Modifications

  1. Command Line Handling

    1. Extension of Command Line Parameter Handling (Leo Caves)

      A command line parameter token can now be a string rather than just one of the single characters 0-9 and A(a)-Z(z). For substitution, a token is indicated by the use of the @ character as before. The token is end-delimited by any non-alphanumeric character. In the case that the token is not found in the parameter table, a check is made to see if the first character of the token is itself a token in the parameter table. If this single character token is in the table, the corresponding value is substituted – this is the necessary scheme to allow backwards compatibilty with the old parameter substitution, which allowed parameters embedded in strings. For unambiguous token detection, “protect” the token with brackets {} — this allows for the use of non alphanumerics in tokens such as -, _.

    2. New Parsing Options (Bernard R. Brooks)

      The IF command will be expanded to allow commands such as:

      IF ?ENER .GT. ?VDW  THEN GOTO label
      
      or
      
      IF ?NSEL .LT. 8 THEN GOTO label
    3. MSCNUM (Bernard R. Brooks)

      New code for flexible miscellaneous command substitutions has been fully incoporated. Additional types were needed to make this code more flexible. Three types are supported, REAL(*8), INTEGER, CHARACTER. There are three subroutines which can be called; integer (SETMSI), character (SETMSC), and real (SETMSR) to specify a command substitution variable. Now it is possible for ?NATOM to return an integer, ?RSM to return a real number, and ?SEGID to return the segment identifier of the first selected atom.

  2. QUANTUM

    Quantum mechanical and molecular mechanical combined force field method was implemented by employing the semi-empirical SCF method of the MOPAC program in the CHARMM version 22. The QUANTUM code has been modified extensively to meet CHARMM standards.

    There were several problems with the quantum code that have been fixed. The van der Waal group nonbond list was missing due to an improper interpretation of the group-group exclusion list in CHARMM (It’s a two state list, not a 3 state as in the atom-atom exclusion list). All vdw interactions between QM and MM group where any QM atom had an exclusion or a 1-4 interaction with any MM atom were not computed. This caused major problems in certain situations where there was a strong electrostatic attraction with no compensating vdw interaction.

    New code to add link and place link atoms has been written.

  3. Frequency Based Crystal Update (Ryszard Czerminski)

    The modification allowes for automated, frequency based, crystal update. New variable (IXTFRQ) is introduced which controls frequency of the crystal update.

  4. Ability to Linearly Increase/Decrease Pressure (Ryszard Czerminski)

    The goal was to allow for linear increase (decrease) of the pressure during single dynamic run. New variables/keywords were introduced (PIXX - initial value of XX component of pressure tensor, PFXX - final value etc... for other components).

  5. Atom Selection

    1. Atom Parse (Bernard R. Brooks)

      A new atom name parsing subroutine has been developed. This makes the code simpler and facilitates further advancements in atom parsing. One new feature allows an atom selection to be used to select a series of atoms. This is very useful in CORREL for specifying clusters of atoms for analysis. When the atom selection feature is used to specify 4 atoms of a dihedral, the first 4 selected atoms will be chosen.

    2. New Tokens (Bernard R. Brooks)

      • new operator; .BYGROUP. <factor>
      • new token; IGROup  <int1> : <int2>

      have been added to allow the selection of atoms based on electrostatic groupings.

      Several keynames have been added to allow the query of the characterstics of selected atoms;

      ?SELATOM  - number of first atom selected
      ?SELIRES  - number of first residue selected
      ?SELISEG  - number of first segment selected
      
      ?SELTYPE  - name of first atom selected
      ?SELRESI  - resid of first residue selected
      ?SELSEGI  - segid of first residue selected
      ?SELRESN  - residue type of first atom selected
      ?SELCHEM  - chemical type of first atom selected

      These new keywords are in addition to the existing keyword;

      ?NSEL    - Number of atoms selected
  6. Correlation

    1. New MANTim Options in CORREL (Bernard R. Brooks)

      A histogram option to time series manipulation has been developed. This is executed by the command;

      MANTime time-series-name HISTogram min-value max-value num-steps

      The selected time series is replaced with a histogram which contains the probability of finding the time series within a given value range. Also, new options (RATIo and KMULt) added to the CORREL MANTIME command.

    2. Dihedral Time Series in CORREL (Bernard R. Brooks)

      Fixed problems with the diheral code in correl to account for torsional timeseries. The correct fluctuation is now determined. The extra processing has been removed from the SHOW command because the data may no longer be valid for this processing when MANTIME commands are present in a script. A new command option “MANTime CONTinuous-dihedral” has been added to allow a dihedral timeseries to be unfolded to a continuous function.

    3. Extension of Solanal ANALysis command (Arnaud Blondel)

      A command -CROSs- was added to allow a cross analysis on two selected subsets of atoms. For the moment the exclusion of the couple of atoms belonging to the same SEGId is not implemented. The keyword CROSs cannot be selected with the following options: WATer, SITE, IKIRkg, ISDIst, IFDBf. IVAC, IMSD and IFMIn have not been tested with CROSs.

  7. SCALAR Command Enhancement (Bernard R. Brooks)

    The ASP arrays (IGNOre, ASPV and VDWS) are now accessible. There is a sort option for the SHOW command. There is a new MASS keyword for the STATistics and AVERage commands

    A new SCALAR READ option has been added. It allows values to be entered from a file. The use is:

    OPEN READ CARD UNIT 12 NAME file.dat
    SCALar WMAIn READ 12 SELE ... END

    which will read selected entries to the weighting array.

  8. SURFACE (Bernard R. Brooks)

    New analytic surface area code and energy terms for ASP (Atomic Solvation Parameters) energy and forces have been fully integrated (and parallelized for multi-machines). This has been achieved by the incorporation and adaptation of the code from Wesson and Eisenberg. The default for the COOR SURFace command is now the analytic surface area. The anaylitic answer is less expensive and more accurate. The older Lee and Richard’s algorithm may still be invoked by specifying a nonzero RPRObe value. The maximum number of contacts that a sphere may have has been increased from 15 to 35.

  9. QAUGMENT (Bernard R. Brooks)

    It is desirable for a patch to be able to augment the charge of an atom. The current code could only set a charge. The new code can add or subtract a value from the charge. This is done by using a patch charge value near 100.0. For example, a charge of 100.15 will add 0.15 to the current charge. A charge value of -101.0 will subtract 1.0 from the current charge. Charge values less than -90.0 or larger than 90.0 are no longer allowed for generate or patch without charge augment. It allows more flexible patches to be developed where the prior charge on modified atoms need not be known.

  10. COORdinate Commands

    1. VACUUM_OP: COOR SEARCH Subcommand (Bernard R. Brooks)

      The ability to manipulate pixel bitmaps generated from the COOR SEARCH command has been developed. The new syntax for the COOR SEARCH command is;

      COOR SEARch {PRINt [UNIT int]} {            } {[VACUum]} {[RESEt]} [SAVE]
                  {[NOPRint]       } {[RCUT  real]} { FILLed } { AND   }
                                     {[RBUFf real]} { HOLES  } { OR    }
                                                               { XOR   }

      The new keywords are;

      SAVE

      save the resultant bitmap for subsequent operations

      AND

      logical AND the new bitmap with the previously saved map

      OR

      logical OR the new bitmap with the previously saved map

      XOR

      logical XOR the new bitmap with the previously saved map

      HOLES

      search for holes (vacuum points surrounded by filled points)

    2. New COOR DIST command (Bernard R. Brooks)

      The COOR DISTance command has been overhauled and has additional features. One such feature is the ability to get g(r) plots from trajectory files using atom selections. It has several other features. The new syntax is:

      COOR DISTance
      
          {  WEIGhting vector-spec               atom-selection           }
          {                                                               }
          { [UNIT int] [CUT real] [ENERGy [CLOSe]] 2X(atom-selection) -   }
      
                  { [Nonbonds] } { [NO14exclusions] } { [NOEXclusions] }  -
                  { NONOnbonds } {    14EXclusions  } {    EXCLusions  }
      
               [TRIAngle]   [ HISTogram HMIN real HMAX real HNUM integer  -
                               [HSAVe] [HPRInt] [HNORm real] [HDENsity real] ]
  11. JOIN/RENUMBER Command (Bernard R. Brooks)

    A “JOIN segid RENUMBER” feature is added in the JOIN command. This allows resid’s to be made sequential within a single segment.

  12. PREFX.SRC overhauled. (Bernard R. Brooks)

    The PREFX program has been overhauled. The new code has the following features:

    • It allows ”!” comments at the end of valid FORTRAN statements.

    • Conversion to single precision is performed ONLY if the SINGLE keyword is present.

    • It allows the use of identifier comments in ## statements. For example:

      ##IF PERT (pertprint)
      ...
      ##ELSE (pertprint)
      ...
      ##ENDIF (pertprint)
      

    This makes the code easier to read and allows ##ENDIF statements to be uniquely identified. A fatal error is flagged if the identifiers do not match.

Major Enhancements and Developments in CHARMM24

During the C24 development cycle, February 15, 1994 to February 15, 1996, we made two bugfix-updates in the c23 releases and three alpha versions and one beta version in the c24 development line. c24x1 is the MMFF implementation in CHARMM developed at the Molecular Simulations Inc.

CHARMM23.0
     c23f4    Release           August    15, 1994
     c23f5    Release           March     15, 1995

CHARMM24.0
     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

Only bugfixes are incorporated into CHARMM23 and all new developments and enhancements have been carried out with the CHARMM24 developmental versions. All modifications are thoroughly recorded in the ChangeLog.c24 file and the following is the summary of new features and major enhancements in CHARMM 24.

New Features in CHARMM24

  1. New Ports and Parallel Versions

    1. Enhancement to Parallel Code (Bernard R. Brooks and Milan Hodoscek)

      There has been continued development of the parallel code for CHARMM. This includes new features run in parallel, new machine types supported, new parallelization methods, and code made to run more efficiently. Due to conflict in routine names with library routines, the subroutines: WRITEC and READC had to be renamed.

      Initial code to allow the use of the Terra parallel computer has been added. Added preflx keyword SGIMP for multiprocessor SG machines using PVM massage passing library. The difference between PVM and (SGIMP, PVM) is that all the processes are spawned on one host and some communication parameters are not supported on MP machines. It can be used on a single processor SG for testing purpose. Use PVM only on a cluster of any type of workstation.

    2. Convex Exemplar SPP-100 and generic PVM Ports (Charles L. Brooks, III and Stephen H. Fleischman)

      A port of CHARMM version 24a2 to general PVM based parallelism using existing parallel code as well as a port to the Convex parallel machine are included.

    3. Cray T3D Port (Charles L. Brooks, III and Barry C. Bolding)

      A port of CHARMM version 24a2 to the Cray T3D parallel computer using existing parallel code is included.

    4. Port of parallel CHARMM to Convex Exemplar SPP-1000 and generic MPI (Charles L. Brooks, III and Stephen H. Fleischman)

      A port of CHARMM version 24a3 to general MPI based parallelism using existing parallel code as well as a port to the Convex parallel machine are included.

    5. Thinking Machine’s CM5 Port (Robert Nagle)

      Previous communication scheme was based on a simple send and receive model. By using TMC’s active message layer, communication bandwith can be increased by anywhere from 50% to 5X.

    6. OS/2 Port (Stefan Boresch)

      CHARMM (c23f4 and c24a3) has been ported to the OS/2 operating system, version 2.x and higher. The Watcom Fortran compiler (v. 9.5, patch-level (c)) has been used. A new pre-processor keyword, OS2, has been introduced, and all OS/2 related changes hide behind the OS2 keyword. There is currently no install script. Please contact me if you want to build an OS/2 version of CHARMM (boresch@tammy.harvard.edu).

  2. Fast Multipole Code for Electrostatic interactions (Robert Nagle)

    This is an initial implementation of a fast multipole method, based on John Board’s work. A new non-bond option (FMA) has been added. This replaces cut-off parameters with a no cut-off hierarchical technique. The advantages of this method are that you can control the error and that it is amenable to parallelization. FMA is an O(N) technique but the constant is large and so FMA will, in general, be slower for systems of less that 5000 atoms, for the same accuracy.

    Two options, LEVEL and TERMS, govern how many hierarchical levels are used and how many terms are retained in the expansion, respectively. In the method, each box at every level is subdivided into 8 sub-boxes - you should select LEVEL so that the boxes at the lowest (i.e. finest) level contain 10-20 atoms on average: 3 or 4 will be typical choices. You then select TERMS to control the accuracy that you require: 4 will often suffice but I would generally recommend 6 or even 8. See the references in fma for a detailed description of the error bounds.

    NOFMA is the nonbond option which turns off the multipole method. Compilation of FMA is controlled by the flag, FMA, in pref.dat.

    FAST ON is required for this initial implementation. This implementation is not yet parallelized.

  3. Energy Embedding by the Addition of a Higher Spatial Dimension (Elan Z. Eisenmesser / Carol Post)

    The energy embedding technique entails placing a molecule into a higher spatial dimension [Crippen, G. M. & Havel, T. F. (1990) J. Chem. Inf. Comput. Sci. Vol 30, 222-227]. The possibility of surmounting energy barriers with these added degrees of freedom may lead to lower energy minima.

    With the recent success of using four dimensions in the GROMOS force field [Van Schaik, R. C., Berendsen, H. J. C., Torda, A. E., & van Gunsteren, W. F. (1993) J. Mol. Biol. Vol 234, 751-762], creating a similar option in CHARMM should also prove advantageous. Specifically, another cartesian coordinate was added to the usual X, Y, and Z coordinates and was appropriately named FDIM for Fourth DIMension. This implementation has led to alterations in some existing code along with the addition of several algorithms.

  4. DIMB (Diagonalization In a Mixed Basis) Method (David Perahia, Liliane Mouawad, Herman van Vlijmen)

    The DIMB (Diagonalization In a Mixed Basis) method (see L. Mouawad and D. Perahia (1993), Biopolymers, 33, 599) is an iterative method to calculate the N lowest normal modes of molecules. It is especially targeted to do large molecules, since it does not require the full Hessian to be stored in memory or on disk. In short, the method does repetitive reduced-basis diagonalizations in bases that consist partially of the approximate eigenvectors, and partially of Cartesian coordinates. Eigenvectors are saved to file during the process. Before that is done, a new basis is again created, which consists of the approximate eigenvectors at that point + the residual vectors (Lanczos vectors). This accelerates the convergence. A very good property of this method is that the final eigenvectors are as accurate as the user wants them to be, so the results are no different from a full-blown diagonalization.

    Because the method is iterative, it takes longer to converge than a regular diagonalization. Sizewise it can handle almost anything on a moderately sized computer. David Perahia calculated a few dozen modes of Hemoglobin (~600 residues = ~6000 atoms = ~18000 d.o.f.) on a SGI workstation with 90 Mb memory. I have done several calculations on 900 residue systems. The actual time to reach convergence depends on the available memory, the desired accuracy, and the number of requested normal modes.

    One other area where the method saves memory is in the storage of the original Hessian. Since this matrix is usually sparse for large systems, a compressed Hessian is set up, which contains all non-zero elements.

    In addition, I added the option to used this compressed Hessian in the reduced-basis diagonalization option of VIBRAN. Before, the same size limits applied to full diagonalizations and reduced-basis diagonalizations. This should not be: people usually want to do reduced-basis calculations because the molecule is too big for the Hessian to be stored in memory. The option VIBRAn REDUce CMPAct will fill the compact Hessian and form the reduced-basis Hessian from this compact Hessian. Overall, this is a big saving on memory space.

  5. Arithmetic Expression Interpreter (Benoit Roux)

    An interpretor of arithmetic expression has been added to the CHARMM command parser. It is called at the level of the miscellaneous command handling using simply by the word CALC (for calculator). It can be used to evaluate algebraic numerical expression. The command supports all mathematical numerical expression with arbitrary number of nesting of recursive parentheses, e.g.,

    exp[1.0-cos(2*(log(2*pi))**2)/0.5]
    

    The parsing is actually very crude since the expression is translated back and forth between character string and a real variable to handle the logic (there is no real subroutine recursion).

  6. TNPACK Update (Tamar Schlick, Phillipe Derreumaux and Eric Barth)

    The truncated-Newton minimization package TNPACK, developed by T. Schlick and A. Fogelson, has been incorporated into CHARMM and adopted for biomolecular energy minimization. TNPACK is based on the preconditioned linear conjugate-gradient technique for solving the Newton equations. The structure of the problem — sparsity of the Hessian — is exploited for preconditioning.

    Thorough experience with the new version of TNPACK in CHARMM has been described in a paper now in press in the Journal of Computational Chemistry: Applications are reported for a series of molecular systems including Alanine Dipeptide (N-Methyl-Alanyl-Acetamide), a dimer of N-Methyl-Acetamide, Deca-Alanine, Mellitin (26 residues), Avian Pancreatic Polypeptide (36 residues), Rubredoxin (52 residues), Bovine Pancreatic Trypsin Inhibitor (58 residues), a dimer of Insulin (99 residues), and Lysozyme (130 residues). Through comparisons among the minimization algorithms available in CHARMM, we find that TNPACK performs significantly better than ABNR in terms of CPU time when curvature information is calculated by a finite-difference of gradients (the “numeric” option of TNPACK). The CPU gain is 50% or more (speedup factors of 1.5 to 2.5) for the largest molecular systems tested and even greater for smaller systems (CPU factors of 1 to 4 for small systems and 1 to 5 for medium systems). With the analytic option, TNPACK converges more rapidly than ABNR for small and medium systems (up to 400 atoms) as well as large molecules that have reasonably good starting conformations; for large systems that are poorly relaxed (i.e., the initial Brookhaven Protein Data Bank structures are poor approximations to the minimum), TNPACK performs similarly to ABNR.

    TNPACK uses curvature information to escape from undesired configurational regions and to ensure the identification of true local minima. It converges rapidly once a convex region is reached and achieves very low final gradient norms, such as of order 10E-8, with little additional work. Even greater overall CPU gains are expected for large-scale minimization problems by making the architectures of CHARMM and TNPACK more compatible with respect to the second-derivative calculations.

    This work should be the focus of future developments. Such work involves sparse storage of the Hessian, efficient sparse Hessian/vector multiplications, and separation of the gradient and Hessian calculations.

  7. X-window graphics extensively modified (Richard M. Venable)

    Several new features have been added to the X-window version of CHARMM graphics. This code has also been tested on a wider variety of hardware platforms (for example: SGI). Changes include: double-buffering, clipping, StaticColor, symbol fonts, window title, modified colormap calls, and a misc. Bug fixes in the labeling of the X axis. A NODISPLAY compile option has been added to the X windows version of CHARMM graphics in which only derivative files are produced. The GRAPhics NOWIndow option can be used to generate the same effect at run time.

  8. Minimum Image Periodic Boundary Code (Charles L. Brooks, III, William A. Shirley and Stephen H. Fleischman)

    Simple minimum periodic boundary conditions are added for cubic, truncated octahedra and rhomboidal (dodecahedra) periodicities which augments the image facility and enhances parallel scaling on scalar parallel machines as well as significantly reducing the memory requirements. This code is developed and fully tested for the simulation cells described above when the cell edgelength is the same in all dimensions. The (trivial) extension to non-identical cell sides will be added. However, it is critical to see reasonable performance on all scalar parallel platforms where simulations using images are currently employed that this enhancement be added now.

  9. GAMESS Code (Bernard R. Brooks and Milan Hodoscek)

    The CHARMM-GAMMES interface is under development. The interface part is completed and testing is in progress.

Major Enhancements in CHARMM24

  1. New Dihedral / Improper Dihedral Energy Routines (Arnaud Blondel)

    The previous energy routines used the derivatives d(cos(phi))/dr to calculate the forces and the second derivatives. This choice introduced an artificial singularity at sin(phi)=0.

    The new routines use the derivative d(phi)/dr and thus have no singularities. This removes the tests to avoid numerical overflow or the switch functions in the vector improper routines.

    The new dihedral routines now support cases where planar conformation is not an extremum. Thus a value other than 0 or 180 can be specified in the dihedral parameters. The dihedral constraints can also use the dihedral functional form using the key word PERIod and giving a non-zero number.

  2. Extended Pressure System, Langevin Piston Code (Bernard R. Brooks, Scott E. Feller and Yuhong Zhang)

    The constant pressure code has been overhauled. The old method based on Berendsen’s method has been replaced with a Langevin Piston Method. When no friction is applied, this method becomes the standard method based on Nose and Klein (adapted from Andersen). At the limit of infinite friction with no random force, this reverts to the Berendsen method.

    The unit cell information has been added to the trajectory file format. This implementation required an update to the image and crystal code which cleaned up some ancient problems. Options for including the surface tension (gamma-Area) term is also completed and tested. This has been developed for the accurate simulation of interfacial systems.

  3. Anisotropic Harmonic Restraints (Bernard R. Brooks)

    The global scale factors: “XSCAle”, “YSCAle”, and “ZSCAle” have been added to the “CONS HARM” command. This allows using the CONS HARM to enforce a planar or linear restraint. This feature is also useful for use in conjunction with our COORPLAS program (for generating 3-D coordinates from plastic models).

  4. New RESDistance Facility (Bernard R. Brooks)

    A new facility, RESD, has been created to allow general distance restraints based on a linear combination of distances. This is useful for searching reaction pathways.

  5. New READ PARAm APPEnd Option (Bernard R. Brooks)

    An append option has been added to the READ PARAM CARD command. This allows just a few parameters to be modified without editing an entire parameter file. A modification to the binary parameter file format was necessary. Old binary files may not be appended, but they are still supported.

  6. New READ PSF APPEnd Option (Bernard R. Brooks)

    An append option has been added to the READ PSF command. This allows PSFs to be easily merged to make a larger PSF. No modification to the binary parameter file format was necessary. This option works with both FILE and CARD options.

  7. Best Fit Option to CORREL TRAJectory Command (Bernard R. Brooks)

    The TRAJectory command in correl now accepts an ORIENt keyword with an optional [MASS] qualifier in conjunction with a second atom selection that will best fit selected atoms with respect to the rms deviation from the reference structure (in the comparison coordinate set). This operation is done prior to the determination of any time series value. This operation will not affect any time series value that is based only on relative distances and angles.

  8. QM/MM Exclude Group Option (Bernard R. Brooks)

    An option EXGRoup has been added which causes all atoms in the group of the link atom host to be excluded from the QM/MM electrostatic interaction terms. Code for specifying the charge of link atoms and their placement has also been added.

  9. Enhancements to the Ewald Code (Bernard R. Brooks, Scott E. Feller and Steve Bogusz)

    The EWALD electrostatic option now runs efficiently for parallel architectures. Also, the maximum K-space values can be specified independently for each direction. Several bugs were fixed. Additional ways to compute ERFC() were added, including a lookup table.

  10. MMFP/SSBP Upgrade (Benoit Roux and Dmitrii Beglov)

    The Miscellaneous Mean-Field Potentials (MMFP) has been upgraded. The spherical solvent boundary potential (SSBP) has also been incorporated into EPERT. A new “membrane-like” planar potential has been introduced using Gaussians to provide a smooth free energy function based on hydropathy profile of individual amino acids and solvent exposure. This is useful to orient membrane proteins. A new primary shell of hydration has been added to the MMFP facility to provide one layer of solvent around a flexible polypeptide. For more information, see Beglov & Roux, Biopolymers 35: 171-178 (1995).

    A solvent boundary potential for the simulation of water at constant pressure is also added to the Miscellaneous Mean Field Potential module. The boundary potential is an approximation but follows from a rigorous statistical mechanical treatment of the boundary. In light of the difficulties raised by the previous treatments, a different route was chosen to formulate and develop the solvent boundary potential for computer simulations of a finite representation of an infinite bulk system. The present theoretical formulation is based on a separation of the multidimensional solute-solvent configurational integral in terms of n “inner” solvent molecules nearest to an arbitrary solute, and the remaining “outer” bulk solvent molecules.

    This formulation, which differs significantly from previous treatments, provides further insight into the statistical mechanical basis of the solvent boundary potential and is helpful in constructing useful approximations for computer simulations in dense liquids. An approximation to the solvent boundary potential is constructed for simulations of bulk water at constant pressure, including the influence of van der Waals (done with RISM) and electrostatic interactions (done with a Kirkwood-like multipole expansion). The approach has been tested with success on several typical systems (water, ions, n-butane and alanine dipeptide).

  11. Upgrade of the NMR module (Benoit Roux)

    The NMR module is upgraded to have better output style. The old version used the value of PRNLEV to choose the printed quantities. Since this was a non-standard style in CHARMM, a series of logical flags have been included in the command calls to print some chosen quantities. In addition, the chemical shift anisotropy (CSA, used in solid state NMR of membrane proteins in oriented samples) has been redefined in term of a zmatrix to prevent confusion. The deuterium quadrupolar splittings (DQS) command is also upgraded. A bug in a call to NORMAL was fixed.

  12. New Options to CORREL (Lennart Nilsson)

    Two new MANTime options have been added to CORREL: CROS and DOTP. CROSsprod name Q(T) = Q(T) x Q2(T) produces the 3D crossproduct of the two 3D vectors formed by the selected and named timeseries and DOTProd name Q(T) = x-comp of Q(T)= Q(T) . Q2(T) gives x-comp of Q2(T) angle in degrees between the two vectors.

  13. The COOR HBONd Command (Lennart Nilsson)

    An option for the analysis of H-bond patterns from trajectories has been added to corman.

    COORdinates  HBONd 2X(atom-selection) [CUT <real>] [CUTA <real>]
             [IUNIt <int>]  [BRIDge <resnam>]
             [FIRSt int] [NUNIts int] [NSKIp int] [BEGIn int] [STOP int]

    The HBONd command analyses a trajectory for hydrogen bonding patterns. For each acceptor/donor in the first selection the average number and average lifetime of hydrogen bonds to any atom in the second selection is calculated. A hydrogen bond is assumed to exist when two candidate atoms are closer than the value specified by CUT (default 2.4A, (reasonable criterion, DeLoof et al. (1992) JACS 114, 4028), and if a value for CUTAngle is given the angle formed by D-H..A is greater than this CUTAngle (in degrees, 180 is a linear H-bond); the default is to allow all angles. The current implementation assumes that hbonding hydrogens are present in the PSF and also uses ACCEptor and DONOr information from the PSF to determine what pairs are possible.

    If output is wanted to a separate file the IUNIt option can be used. If the BRIDge option is used the routine calculates average number and lifetime of bridges formed between all pairs of atoms in the two selections; a bridge is counted a residue of the type specified with the BRIDge <resnam> hydrogen bonds (using same criteria as for direct hbonding) to at least one atom in each selection. The typical use of this would be to find water bridges. Here again, results are presented for each atom in the first selection.

    In order not to find hbonds between bonded atoms UPDATE is called, which requires coordinates to be present when invoking this module. Since this is done just to get the non-bond exclusion lists, the cut-offs are set to very small values, and could influence subsequent energy evaluations if the non-bond cutoffs are not then respecified.

  14. NORESET Option for SHAKE (Lennart Nilsson)

    The NORESET option is added to allow multiple shake commands. It is useful to be able to define shake on bonds, bonh or so on several different sets of atoms, with different shake options. The NORESET keyword to shake command allows this by not zeroing counter.

  15. Trajectory Reading (Lennart Nilsson)

    READCV is modified to read coordinates at multiples of skip FROM the actual first coordinate set in a trajectory file.

  16. Make BLOCK work with IMAGE/CRYSTAL and vice versa (Stefan Boresch)

    In order to make BLOCK work / coexist with the IMAGE module two things had to be changed: (1) A memory allocation problem in the BLOCK datastructure and (2) the post-processing modules needed to be overhauled to allow for nonbonded list updates while reading frames from the trajectory.

    Ad (1), memory allocation: BLOCK uses two data-structures, one containing the interaction matrix between blocks, and one containing the block number for each atom (IBLCKP). This array was allocated so far as INTEG4(NATOM) on the heap. However, when IMAGE atoms are present, the energy routines attempt to find out to which block an IMAGE atom belongs. This at one point or the other causes a memory access violation. The solution consists out of two parts. (i) The IBLCKP data-structure is now allocated as INTEG4(MAXAIM) on the heap; therefore there is always enough space provided. (ii) The entries for the IMAGE atoms have to be initialized, and this has to be done at EVERY image update. However, similar things are already done for a number of other quantities like masses, vdW params, charges etc. All this is done among a number of other things in subroutine MKIMAT in upimag.src, where I have added an appropriate statement.

    Ad (2), changes to post-processing routines: Real/Image atoms leave/enter the simulation box/system dynamically. Therefore, the nonbonded/image interaction lists have to be updated during post-processing. The hooks were already in the program, subroutine BLUPLST. The real changes hide in this routine, most changes in BLFREE, BLEAVG and BLCOMP are either cosmetic or ensure proper printout. Post-processing routines FREE, EAVG and COMP will actually print IMAGE terms if present. The routine BLUPLST is a sibling of routine updeci in heurist.src. The heuristic update scheme itself is removed, as I feel that one should update the lists at every frame. Also, the CRYSTAL specific section of UPDECI is not present in BLUPLST as I don’t understand it. Therefore, care should be exercised when using BLOCK with CRYSTAL! Negative values of INBFRQ/IMGFRQ are trapped, in this case they are set to 1; Printout from the update / list generation routines is suppressed by temporarily raising the PRNLEV to 1.

    The BLOCK documentation (BLOCK) has been revised and reflects these modifications. A new testcase block3.inp has been added to test/c24test.

  17. Constraint correction for PERT (Stefan Boresch)

    The current version of PERT cannot handle situations where SHAKE is applied to bonds which change in length due to an alchemical mutation as SHAKE and PERT do not “communicate”. Furthermore, in such cases a constraint correction has to be computed and added to the free energy difference. Two steps are required to fix this problem:

    1. The constraint list needs to be updated as a function of the coupling parameter lambda.
    2. The constraint correction has to be calculated.

    Only thermodynamic integration (both for slow-growth and windowing) is supported; the exponential formula will give nonsense results. (If someone wants to fix this, please look at Pearlman/Kollman, JCP 1991, 94, 4532 and Severance et al. J. Comput. Chem. 1995, 16, 311.)

    The method to calculate the constraint corrections is based on extracting the respective Lagrangian multipliers from the SHAKe routine; this approach is briefly described in van Gunsteren et al. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; ESCOM: Leiden 1994; Vol. 2, pp 315-348. The approach fully includes inertial contributions, it is left to the user to account for those correctly in the context of the problem.

    The new code is mostly transparent and does not really require additional documentation. However, some information is added to Free Energy Perturbation Calculations. A new testcase pert2.inp is also added to test/c24test.

  18. Non-Cubic Crystal Building Problem Fix (Wonpil Im and Ryszard Czerminski)

    The crystal build facility uses the symmetrized rotated shape matrix XTLABC obtained from lattice parameters. However, it does not apply the same rotation to the unit cell moiety, which may result in bad contacts in non-cubic crystals. The problem is fixed by calling the subroutine ROTXTL. Some tests for the rotation are added by Ryszard.

Major Enhancements and Developments in CHARMM25

During the C25 development cycle, August 15, 1995 to August 15, 1997, we made three bugfix-updates in the c24 releases and three alpha versions and one beta version in the c25 development line.

CHARMM24.0
     c24b2    Release           February  15, 1996
     c24g1    Release           August    15, 1996
     c24g2    Release           February  15, 1997

CHARMM25.0
     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

Only bugfixes are incorporated into CHARMM24 and all new developments and enhancements have been carried out with the CHARMM25 developmental versions. All modifications are thoroughly recorded in the ChangeLog.c25 file and the following is the summary of new features and major enhancements in CHARMM 25.

New Features in CHARMM25

  1. Merck Molecular Force Field (MMFF) (Thomas A. Halgren, Ryszard Czerminski, Jay L. Banks, Bernard R. Brooks, and Youngdo Won)

    Merck Molecular Force Field (MMFF) developed by Tom Halgren at Merck has been implemented in CHARMM. Ryszard introduced MMFF into c23f2, which made the c24x1 (February 15, 1994) version for evaluation. As CHARMM was evolved through the c24 development project, Jay incorporated MMFF into c24b1 in a less intrusive manner. Bernie and other developers reviewed c24b1/MMFF and suggested some corrections. Youngdo took the Jay’s code and Bernie’s suggestions and made the checkin code of MMFF. MMFF is documented in doc/Merck Molecular Force Field (MMFF94).

  2. CADPAC (Paul Lyne)

    An interface is added to allow CHARMM to run with CADPAC6.0 when performing QM-MM calculations. CADPAC6.0 can perform HF, MP2, MP3 and DF calculations.

  3. Particle Mesh Ewald Code (Bernard R. Brooks)

    The Particle Mesh Ewald (PME) method has been implemented. This code is based on code sent by Tom Darden at NIEHS/NIH. It has been modified so as to conform with CHARMM coding standards. This version is much faster than the standard Ewald code and accuracy does not appear to be a problem when reasonable options are used. This code uses the new “smooth” algorithm. See The Ewald Summation method for more details.

    The code is now running in parallel and the following features are supported:

    • PERT (free energy calculation) with PME (including pressures)
    • Assymetric units with CRYSTAL (when NOPEr>0 in CRYStal BUILd command) is now supported with PME.
    • Total charge (Qtot<>0) energy and pressure correction term has been added.
    • Accurate pressures for the triclinic (and all other) cases (and for PERT)
    • Ewald energy components have been separated and can be turned off with the SKIP command (‘EWKS’,’EWSE’,’EWEX’,’EWQC’,’EWUT’). (k-space,self term,exclusion,total Q correction,utility)
  4. External Force to Selected Atoms (Lennart Nilsson)

    A new command has been added which calculates a new energy term corresponding to a static or periodically varying external force on an atom selection.

  5. Distance matrix and radius of gyration restraints (Charles L. Brooks, III, Felix B. Sheinerman and Erik Boczko)

    New restraint energy terms added to permit restraint of system based on its radius of gyration and/or the value of a reaction coordiante what describes the degree of nativeness based on the number of native side chain contacts. New Keywords are RGYCONS and DMCONS.

  6. HTML Doc Files (Rick Venable and Charles L. Brooks, III)

    Added html documentation files and developed/modified doc2html.com originally developed at NIH. All relevant files added to support/htmldoc

Major Enhancements in CHARMM25

  1. PARALLEL CODE reorganized and extended (Milan Hodoscek, Charles L. Brooks)

    The parallel code has been updated and organized into three parts: paral1.src, paral2.src and paral3.src. The new code is faster and there has been a significant additions to support other platforms. We now support about 15 platforms including ALPHAMP, T3D, T3E, Terra, Global-Works-Server and others.

  2. Linux Port (Milan Hodoscek)

    The Linux port is done with the GNU Fortran compiler, version 0.5.18. For now, all Linux related changes are under the GNU keyword.

  3. Nonbond Energy Code Overhaul with Semi-Automatic Code Expansion (Bernard R. Brooks)

    The program PREFLX (PREFX) has been overhauled to allow semi-automatic code expansion in the moving of inner loop if-tests to the outside of do-loops. The nonbond energy routines are cleaned and organized to utilized the semi-automatic expansion. Obsolete ZTBL code is removed.

  4. Ewald code (Bernard R. Brooks)

    Memory needs of the EWALD electrostatic option have been reduced, and multiple parallel options are now supported. Pressure code has been fixed as well.

    The calling sequence to ENBOND was modified so that a flag (QEWEX) can be sent indicating whether the nonbond exclusion correction should be performed for the Ewald calculation. This corrects several problems (such as Ewald with MTS and Ewald with PERT) and this simplifies some code relative to the handling of the exclusion lists. Also there were several changes to EPERT so that the Ewald method will report a correct internal virial (for pressure). The Ewald method was enabled for the GROUP option so that group lists can be used. This reduces the amount of memory and the time needed to handle the nonbond lists (good for limited memory parallel machines).

    A version of EWALD was developed for MMFF. The usual MMFF electrostatic term: qq/(r+d) is split into two terms: qq/r - qq*d/(r*(r+d)) The first term is handled by the Ewald method in the usual manner (real-space and k-space parts) and the second term is truncated at the cutoff distance using a switching function (from CTONNB to CTOFNB). Since the second term is quite small at the cutoff distance, the use of a switching function should not introduce significant artificial forces.

  5. Restrained Distance Code Enhancement (Bernard R. Brooks)

    The restained distance method has been extended to allow the use of a one sided function (positive or negative). It also allows a non-unit exponent for the individual distance terms. The code is now much more general in its ability to define distnace based retraints based on multiple distances.

  6. COOR DIPOLE (Bernard R. Brooks)

    A COOR DIPOle command has been added. This command computes tha charge and dipole (multipoles) for selected atoms.

  7. READ PSF APPEnd (Bernard R. Brooks)

    The READ PSF APPEnd command option has been modified so that it does not initialize the coordinates of existing atoms. Only the new appended atoms will have undefined coordinates.

  8. Replica within Images (Bernard R. Brooks)

    The replica code has been enhanced so that it workes with images and the crystal facility.

  9. The crystal facility has been extended (Bernard R. Brooks)

    The follwing new features have been added:

    • The “DODE” has been renamed “OCTA” (for truncated OCTAhedron). (pressure bug fixed for OCTA)
    • A new type “RHDO” has been added (for RHombic DOdecahedron).
    • The CRYSTAL BUILD command is now much faster and more accurate. The use of the double atom search has been limited.
    • The documentation has been updated to give detailed information regarding crystal types.
    • The WRITe/PRINt IMAGE command is no longer iterative (in accord with the existing documentation).
  10. Overhaul of Harmonic restraints (Bernard R. Brooks)

    The CONS HARM command has been overhauled and extended. The new syntax has three different types of harmonic restraints:

    CONStraint HARMonic { [ABSOlute]  absolute-specs    }  force-const-spec
                        {  BESTfit    coordinate-spec   }
                        {  RELAtive  2nd-atom-selection }
                        {  CLEAr                        }

    The ABSOlute is the old method. The BESTfit causes the reference set to be logically bestfit rotated/translated before computing the restraint energy. The RELAtive allows two portions of one PSF to be restrained to the same internal geometry by the bestfit least squares rotation (no reference coordinates used).

    Some features and changes:

    • Multiple restraints (same or different types) are allowed.
    • HARMonic restraint I/O is no longer supported.
    • The old command syntax still functions (no rewrite of scripts required).
    • The READ/PRINt/WRITe CONS commands now have a “PSF 0” option for PERT.
    • PERT supports all of these restraint types.

    Restriction:

    • Each atom may participate in AT MOST one harmonic restraint term.
  11. Enhancement to REPLICA/PATH (Bernard R. Brooks)

    The REPLICA/PATH method has been extended to allow for bestfit translation and/or rotations between adjacent replicas before computing the restraint energies. Getting the forces right was the hard part. This allows entire molecules to be replicated (or sections with significant freedom).

    RPATh  [ KRMS real ] [ KANGle real ] [ COSMax real ] [MASS] [WEIGht]
                 [ KMAXrms real ] [RMAXrms real ] [ ROTAtions ] [ TRANslations ]
  12. CHARMM/GAMESS enhanced (Milan Hodoscek)

    The version of GAMESS has been updated to the March-97 version from Ameslab. Also, QM/MM gaussian blur of MM charges has been implemented as an option.

  13. A few small changes to MMFP and NMR (Benoit Roux)

    A few small changes to some MMFP subroutine have been made. The main thing is a second atom select for the SSBP command that allows the present of atoms outside the boundary radius. This could be useful when the boundary is used only for an active site. The relaxation time due to the chemical shift anisotropy addition has been added to NMR.

  14. COOR DMAT (Charles L. Brooks, III)

    The dist keyword has been removed from the covariance command and a new analysis command has been added under the coor subsyntax. This command is accessed with the command COOR DMAT and provides some general tools for the calculation, manipulation and storage/extraction of distance matrix based properties. This routine has some overlap with the new distance command introduced by Bernie Brooks but also provides significant complementarity in extending the range of properties computed.