CHARMM c28a3 gamess-uk.doc

File: GamessUK ]-[ Node: Top
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      Combined Quantum Mechanical and Molecular Mechanics Method
                    Based on GAMESS-UK in CHARMM

                            Paul Sherwood

          based on the GAMESS(US) interface from Milan Hodoscek

     Ab initio program GAMESS-UK (General Atomic and Molecular Electronic
Structure System, UK version) is connected to CHARMM program in a QM/MM
method.  This method is based on the interface to the GAMESS (US version),
the latter being an 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.

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


GAMEss   [REMOve] [EXGRoup] [QINPut] [BLURred] (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!

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.

        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: GamessUK ]-[ Node: Usage
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CHARMM input scripts are the same as before except the addition of
ENVIronment commands and the GAMEss command itself. GAMESS-UK commands are in a
separate file call, (or with an alternative name indicated by the
"" environment variable. The GAMESS-UK input file has the same structure
as it would have for a normal GAMESS-UK run, except that the specification of
the geometry is omitted.

        Names of the files for GAMESS-UK are specefied with environment
variables as follows. It is essential to provide a routing for ed3 to 
ensure it is available to hold information between GAMESS-UK calls,
other file specifications are optional.

     use ENVIronment command inside CHARMM
     envi "ed2"   "/scratch/user/test.ed2" ! quotes needed for lowercase names
     envi "ed3"   "/scratch/user/test.ed3"
     or use (t)csh
     setenv ed2     /scratch/user/test.ed2
     setenv ed3     /scratch/user/test.ed3
     or ksh,sh,bash
     export ed2=test.ed2
     export ed3=test.ed3

     or within GAMESS-UK, use the file predirective
     file ed3 /scratch/user/test.ed3
     file ed2 /scratch/user/test.ed2

	It is advised that the GAMESS-UK directives

	noprint dist anal

	is strongly recommended as these diagnostic calculations
don't contribute to the charmm job but use a lot of memory
when there are a lot of classical atoms.

	You can use the "gamess.out" environment variable to 
control the routing of the GAMESS-UK output, or you can define
it as stdout as follows (csh version):

	setenv gamess.out stdout

in which case the GAMESS-UK output will be mixed with the charmm
output.  (Note these don't seem to work with the bash shell, as
the export command doesn't accept variable names containing a
period (.), we will have to change this part of the code.

	Make sure the gamess input contains a generous time
card, since the GAMESS calculation will be skipped if
it thinks it has run out of time.

	If you see that the quantum part of the energy goes to
zero, it may reflect the timeout condition above, or some
other non-fatal problem in GAMESS-UK. Check the GAMESS-UK log

        For complete information about GAMESS input see the CFS web site


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



        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/c28test/guktst.inp]


File: GamessUK ]-[ Node: Installation
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        Installation itself cannot be automated yet so one has to
follow this procedure (if there are any problems ask

1.        Unpack the GAMESS-UK distribution as a subdirectory of gukint:

2. <machine-type> <size-keyword> U <other-options>

The build procedure works by executing a configuration script within
the GAMESS-UK source tree, (GAMESS-UK/utilities/charmm_configure).
Assuming GAMESS-UK has already been ported to the target platform, it
is this file that will generally need modification on plaforms
for which the CHARMM/GAMESS-UK interface has not been tested.

The following is a summary of the status (c28 release)

Architecture   CHARMM host     Parallel    Status
               keyword         Options

SGI R4400      sgi             -           OK
Pentium/Linux  gnu             -           OK

Porting Notes

It is necessary to ensure that charmm_configure issues the
configure command with a valid set of keywords, the most
important on being the machine type. Unfortunately there isn't
a one-to-one mapping between CHARMM host types and GAMESS-UK
machine types.   

e.g. for charmm host type = alpha, gamess type should be 
axpev5 or axpev6 etc (depending on the processor type).
In the short term, customisation of the charmm_configure
script will be needed.

Similarly, changes to charmm_configure may be needed to
request the required GAMESS-UK configuration options for
a parallel build. Probably the best bet for a simple 
parallel GAMESS-UK/CHARMM code is to select MPI with
static load balancing options, for which the "mpi"
keyword needs to be passed to configure. 

On the Cray-T3E, the Global Array port of GAMESS-UK 
can be used, you will need to modify
and Makefile_t3e to load the correct libraries (GA,
MA.... etc).

NB The GAMESS-UK distribution can only support a single architecture
(there are no architecture dependent directories). When moving the
code from one platform to another, be sure to clear out the
object and library files

    % cd source/gukint/GAMESS-UK/m4
    % make clean

When building the parallel code the additional, manual steps
will be needed

For  the MPI code

  - in, set the variables incpath and libpath


  - Some changes may be needed to build/UNX/Makefile_<arch> to support
    loading with the parallel libraries  (e.g. using MPILD)

When building on the T3E (or other platforms for which the
GAMESS-UK port uses the Global Array tools) modify
build/UNX/ to include the list of object files
indicated by ${GASTUFF} and remove ${NONGA}.


File: GamessUK ]-[ Node: Status
Up: Top -=- Next: Top -=- Previous: Installation

GAMESS-UK/CHARMM interface status (July 2000)

- Parallel version is functional, but will require changes to and/or charmm_configure to activate

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

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

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

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