CHARMM c30b1 gamess.doc



File: Gamess ]-[ Node: Top
Up: (commands.doc) -=- Next: Description\n


   Combined Quantum Mechanical and Molecular Mechanics Method
                  Based on GAMESS in CHARMM

                     by Milan Hodoscek
         (milan@par10.mgsl.dcrt.nih.gov,milan@kihp6.ki.si)


        Ab initio program GAMESS (General Atomic and Molecular
Electronic Structure System) is connected to CHARMM program in a QM/MM
method.  This method is extension of the QUANTUM code which is
described in J. Comp. Chem., Vol. 11, No. 6, 700-733 (1990).


* Menu:

* Description::         Description of the gamess commands.
* Using::               How to run GAMESS in CHARMM.
* Installation::        How to install GAMESS in CHARMM environment.
* Status::              Status of the interface code.
* Functionality::       Functionality of the interface code.


File: Gamess ]-[ Node: Description
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        The GAMESS QM potential is initialized with the GAMEss command.

[SYNTAX GAMEss]

GAMEss   [REMOve] [EXGRoup] [QINPut] [BLURred] [NOGUess] (atom selection)

REMOve:  Classical energies within QM atoms are removed.

EXGRoup: QM/MM Electrostatics for link host groups removed.

QINPut:  Charges are taken from PSF for the QM atoms. Charges
         may be non integer numbers. Use this with the REMOve!

NOGUess: Obtains initial orbital guess from previous calculation. 
         Default is to recalculate initial orbitals each time.

BLURred: MM charges are scaled by a gaussian function (equivalent to ECP)
         Width of the gaussian function is specified in WMAIN array 
         (usually by SCALar command)
         The value for charge is taken from PSF. Some values of WMAIN have
         special meaning: 

         WMAIN.GT.999.0 ignore this atom from the QM/MM interaction
         WMAIN.EQ.  0.0 treat this atom as point charge in the QM/MM potential
                

         The atoms in selection will be treated as QM atoms.

        Link atom may be added between an QM and MM atoms with the
following command:


ADDLinkatom  link-atom-name  QM-atom-spec  MM-atom-spec

      link-atom-name ::= a four character descriptor starting with QQ.

      atom-spec::= {residue-number atom-name}
                   { segid  resid atom-name }
                   { BYNUm  atom-number     }

        When using link atoms to break a bond between QM and MM
regions bond and angle parameters have to be added to parameter file
or better use READ PARAm APPEnd command. Also note that QQH type has
to be added in the RTF file (see test/c25test/gmstst.inp).

        If define is used for selection of QM region put it after all
ADDLink commands so the numbers of atoms in the selections are not
changed. Link atoms are always selected as QM atoms.

=======================================================================


File: Gamess ]-[ Node: Usage
Up: Top -=- Next: Installation -=- Previous: Description\n

        In order to run GAMESS and CHARMM on parallel machines I/O of
GAMESS and CHARMM was separated. This is now true even for scalar
runs. CHARMM input scripts are the same as before except the addition of
ENVIronment commands and GAMEss command itself. GAMESS commands are in a
separate file which is pointed to by INPUT environment variable.

        Names of the files for GAMESS are specefied with environment
variables as follows:

     use ENVIronment command inside CHARMM
     
     envi INPUT   "test.gms"          ! quotes needed for lowercase names
     envi OUTPUT  "test.out"
     envi PUNCH   "scratch/test.dat"
     envi DICTNRY "scratch/test.F10"
     envi WORK15  "scratch/test.F15"
     envi DASORT  "scratch/test.F20"
     
     or use (t)csh
     
     setenv INPUT   test.gms
     setenv OUTPUT  test.out
     setenv PUNCH   scratch/test.dat
     setenv DICTNRY scratch/test.F10
     setenv WORK15  scratch/test.F15
     setenv DASORT  scratch/test.F20
     
     or ksh,sh,bash
     
     export INPUT   = test.gms
     export OUTPUT  = test.out
     export PUNCH   = scratch/test.dat
     export DICTNRY = scratch/test.F10
     export WORK15  = scratch/test.F15
     export DASORT  = scratch/test.F20



        For complete information about GAMESS input see INPUT.DOC file in
GAMESS distribution. (NIH: ~milan/gamess/hp/INPUT.DOC)

Example:
--------

GAMESS commands have to be in a separate file. Example for the GAMESS input
follows:

-----------------------------------------------------------------------------
 $CONTRL COORD=CART NOSYM=1 NPRINT=-5    ! This is rarely changed
         SCFTYP=RHF ICHARG=0             ! This usually has to be changed
         RunTyp=Gradient                 ! Normally forces are needed
 !       RunTyp=Energy                   ! If only energy is needed
 $END
 $SYSTEM MEMORY=1000000                  ! memory allocation
         TIMLIM=100000 $END
 $BASIS  GBASIS=N31 NGAUSS=6 $END          
 $SCF    DIRSCF=.True.  $END             ! DIRSCF=.true. recommended
                                         ! if there are convergence problems
                                         ! try SOSCF=.FALSE.
 $DATA
                                         ! This can be empty

 $END
------------------------------------------------------------------------------

        The above is for 6-31G calculation of any neutral molecule.  $DATA
section may be left empty or filled with basis set information in the case
when it cannot be specified by the $BASIS keyword.


[NOTE: For more examples look at test/c25test/gmstst.inp]

==========================================================



File: Gamess ]-[ Node: Installation
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Installation
------------

        Look at the GAMESS home page for instructions how to obtain the code.

        Installation itself cannot be automated yet so one has to
follow this procedure (if there are any problems ask milan@cmm.ki.si):

1.        Put all the source (*.src and *.c) files in source/gamint/gamess

2.        Follow instructions in the begining of the gamess.src file, to
      change:
C
C     ----- CHARMM INTERFACE -----
C     TO USE GAMESS FROM INSIDE OF CHARMM, YOU MUST
C     1. INITIALIZE KCHRMM JUST BELOW TO 1
C     2. CHANGE "PROGRAM GAMESS" ABOVE TO "SUBROUTINE GAMESS"
C     3. CHANGE THE "STOP" STATEMENT BELOW TO "RETURN"
C     4. DELETE DUMMY SUBROUTINES -CHGMIU- AND -CHMDAT- BELOW
C     5. CHANGE -MXCHRM- FROM 1 TO 25120 IN ALL PARAMETER DEFINITIONS
C        FOUND IN GAMESS,GRD1,INPUTB,INPUTC,INT1 MODULES

3. install.com <machine-type> <size-keyword> Q <other-options>

The compile scripts are available for the following platforms:

T3E, T3D, IBMRS, IBM/SP, SUN, SGI, HP-UX, Convex SPP, DEC alpha,
PC/Linux with 3 compilers (Absoft, f2c, g77)

==========================================================



File: Gamess ]-[ Node: Status
Up: Top -=- Next: Functionality -=- Previous: Installation\n

GAMESS/CHARMM interface status (July 1996)

- Parallel version is fully functional

- I/O including standard input and output are separated for
  GAMESS.

- All CHARMM testcases are still OK when CHARMM is compiled
  with GAMESS inside.

- GAMESS, CADPAC and QUANTUM keywords cannot coexist in pref.dat

- MNDO, AM1, PM3 hamiltonians work only in pure QM
  calculations. No QM/MM energies and derivatives with this 
  wavefunctions yet.

- GAMESS recognizes atoms by their masses as specified in the 
  RTF file




File: Gamess ]-[ Node: Functionality
Up: Top -=- Next: Implementation -=- Previous: Status\n


The following methods work with the GAMESS/CHARMM
(from GAMESS INTRO.DOC file)

  
       I. A wide range of quantum chemical computations are
          possible using GAMESS in the CHARMM MM field, which
 
             1. Calculates RHF, UHF, ROHF, GVB, or MCSCF self-
                consistent field molecular wavefunctions.
 
             2. Calculates CI or MP2 corrections to the energy
                of these SCF functions.
 
             3. Calculates analytic energy gradients for all SCF
                wavefunctions, plus closed shell MP2 or CI.
 
             4. Optimizes molecular geometries using the energy
                gradient, in terms of Cartesian or internal coords.
 
             5. Searches for potential energy surface saddle points.
 
             6. Computes the energy hessian, and thus normal modes,
                vibrational frequencies, and IR intensities.
 
             7. Traces the intrinsic reaction path from a saddle
                point to reactants or products.
 
             8. Traces gradient extremal curves, which may lead from
                one stationary point such as a minimum to another,
                which might be a saddle point.

             9. Follows the dynamic reaction coordinate, a classical
                mechanics trajectory on the potential energy surface.
 
            10. Computes radiative transition probabilities.

            11. Evaluates spin-orbit coupled wavefunctions.
 
            12. Applies finite electric fields, extracting the
                molecule's linear polarizability, and first and
                second order hyperpolarizabilities.

            13. Evaluates analytic frequency dependent non-linear
                optical polarizability properties, for RHF functions.
 
            14. Obtains localized orbitals by the Foster-Boys,
                Edmiston-Ruedenberg, or Pipek-Mezey methods, with
                optional SCF or MP2 energy analysis of the LMOs.
 
            15. Calculates the following molecular properties:
                   a. dipole, quadrupole, and octupole moments
                   b. electrostatic potential
                   c. electric field and electric field gradients
                   d. electron density and spin density
                   e. Mulliken and Lowdin population analysis
                   f. virial theorem and energy components
                   g. Stone's distributed multipole analysis

            16. Models solvent effects by
                   a. effective fragment potentials (EFP)
                   b. polarizable continuum model (PCM)
                   c. self-consistent reaction field (SCRF)


      II. A quick summary of the current program capabilities
          is given below.

                         SCFTYP= RHF    ROHF    UHF    GVB    MCSCF
                                 ---    ----    ---    ---    -----
          Energy                 CDP    CDP     CDP    CDP     CDP

          analytic gradient      CDP    CDP     CDP    CDP     CDP

          numerical Hessian      CDP    CDP     CDP    CDP     CDP

          analytic Hessian       CDP    CDP      -     CDP      -

          MP2 energy             CDP    CDP     CDP     -       C
 
          MP2 gradient           CD      -       -      -       -

          CI energy              CDP    CDP      -     CDP     CDP

          CI gradient            CD      -       -      -       -

          MOPAC energy           yes    yes     yes    yes      -

          MOPAC gradient         yes    yes     yes     -       -

           C= conventional storage of AO integrals on disk
           D= direct evaluation of AO integrals
           P= parallel execution


   III. The methods listed above which don't have analytic gradients
        are not available for CHARMM minimizations and dynamic
        calculations.


   IV.  The following are available only in the pure QM calculations:

             1. Calculates semi-empirical MNDO, AM1, or PM3
                RHF, UHF, or ROHF wavefunctions.




File: Gamess ]-[ Node: Implementation
Up: Top -=- Next: Top -=- Previous: Functionality\n

Implementation
--------------

This is for version 6 SEP 2001 R3 of GAMESS or later:

The new DDI (Distributed Data Interface) library is used by parallel
GAMESS. This implementation in GAMESS uses 2 threads per CPU, and
client-server model which CANNOT be made compatible with CHARMM
parallel library. The new library was made from scratch and put in
source/gamint/ddi.src, which replaces the ddi.src file in GAMESS
distribution.

The following files need to be removed from gamint/gamess directory:

ddi.src
ddikick.c
ddisoc.c
ddishm.src
vector.src

The following files are modified from original GAMESS:

    gamint/gamess/gamess.src
    gamint/gamess/grd1.src
    gamint/gamess/guess.src
    gamint/gamess/inputa.src
    gamint/gamess/inputb.src
    gamint/gamess/inputc.src
    gamint/gamess/int1.src
    gamint/gamess/iolib.src
    gamint/gamess/mccas.src
    gamint/gamess/scflib.src
    gamint/gamess/zunix.c

Some changes for CHARMM interface into upstream version of the GAMESS
still didn't made it so contact milan@cmm.ki.si for more info.

CHARMM .doc Homepage


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NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute