gamess-uk (c38b1)
Combined Quantum Mechanical and Molecular Mechanics Method
Based on GAMESS-UK in CHARMM
Paul Sherwood
(p.sherwood@dl.ac.uk)
based on the GAMESS(US) interface from Milan Hodoscek
(milan@par10.mgsl.dcrt.nih.gov,milan@kihp6.ki.si)
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).
* 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.
Based on GAMESS-UK in CHARMM
Paul Sherwood
(p.sherwood@dl.ac.uk)
based on the GAMESS(US) interface from Milan Hodoscek
(milan@par10.mgsl.dcrt.nih.gov,milan@kihp6.ki.si)
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).
* 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.
Top
The GAMESS QM potential is initialized with the GAMEss command.
[SYNTAX GAMEss]
GAMEss [REMOve] [EXGRoup] [QINPut] [BLURred RECAll [INT]] (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
RECAll: Use the RECAll array (as specified in scalar.doc) to set BLUR
widths instead of the main WMAIN array. This is necessary when
using Gaussian BLURred MM charges with the Replica Path or NEB
methods as these make use of the WMAIN array. See QM-MM_DGMM.inp
in the test directory for an example.
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.
=======================================================================
The GAMESS QM potential is initialized with the GAMEss command.
[SYNTAX GAMEss]
GAMEss [REMOve] [EXGRoup] [QINPut] [BLURred RECAll [INT]] (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
RECAll: Use the RECAll array (as specified in scalar.doc) to set BLUR
widths instead of the main WMAIN array. This is necessary when
using Gaussian BLURred MM charges with the Replica Path or NEB
methods as these make use of the WMAIN array. See QM-MM_DGMM.inp
in the test directory for an example.
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.
=======================================================================
Top
ENVIronment commands and the GAMEss command itself. GAMESS-UK commands are in a
separate file call gamess.in, (or with an alternative name indicated by the
"gamess.in" 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
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.
GAMESS-UK input file directives
-------------------------------
The GAMESS-UK data is provided in a separate file, which follows GAMESS-UK
format except that there is no coordinates section.
In addition to those directives needed to switch on the reuiqred energy
expresion, you should
1) include "runtype gradient" to force the computation of both energy
and forces (unless you are sure you are not going to invoke any calculation
that requires a gradient from your script).
2)It is advised that the GAMESS-UK directives
noprint dist anal
be included 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.
3) 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.
4) 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
file.
5) The directive "chm" may be added to set CHARMM-specific options
as follows:
chm noatom : request that GAMESS-UK output items that list all
the atoms be suppressed This is important for macromolecular
systems.
chm append : request that all outputs be concatenated (the default
is that you will only save the last one)
chm offset : provide an energy offset to be added to all the QM
energies. This can help ensure the values print within
the fields expected in CHARMM.
chm debug : diagnostic print (not recommended unless developing)
Example:
--------
GAMESS commands have to be in a separate file. Example for the GAMESS input
follows:
-----------------------------------------------------------------------------
core 5000000
chm append
chm noatompr
chm offset 100
title
qm region for charmm
charge 0
adapt off
nosym
noprint distance analysis
basis 6-31g
scftype rhf
runtype gradient
vectors atoms
enter 1
The above is for 6-31G calculation of any neutral molecule.
[NOTE: For more examples look at test/c28test/cquantumtest/]
For complete information about GAMESS input see the CFS web site
http://www.dl.ac.uk/CFS.
For further information and updates on CHARMM/GAMESS-UK interface
see http://www.cse.clrc.ac.uk/qcg/chmguk
==========================================================
ENVIronment commands and the GAMEss command itself. GAMESS-UK commands are in a
separate file call gamess.in, (or with an alternative name indicated by the
"gamess.in" 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
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.
GAMESS-UK input file directives
-------------------------------
The GAMESS-UK data is provided in a separate file, which follows GAMESS-UK
format except that there is no coordinates section.
In addition to those directives needed to switch on the reuiqred energy
expresion, you should
1) include "runtype gradient" to force the computation of both energy
and forces (unless you are sure you are not going to invoke any calculation
that requires a gradient from your script).
2)It is advised that the GAMESS-UK directives
noprint dist anal
be included 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.
3) 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.
4) 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
file.
5) The directive "chm" may be added to set CHARMM-specific options
as follows:
chm noatom : request that GAMESS-UK output items that list all
the atoms be suppressed This is important for macromolecular
systems.
chm append : request that all outputs be concatenated (the default
is that you will only save the last one)
chm offset : provide an energy offset to be added to all the QM
energies. This can help ensure the values print within
the fields expected in CHARMM.
chm debug : diagnostic print (not recommended unless developing)
Example:
--------
GAMESS commands have to be in a separate file. Example for the GAMESS input
follows:
-----------------------------------------------------------------------------
core 5000000
chm append
chm noatompr
chm offset 100
title
qm region for charmm
charge 0
adapt off
nosym
noprint distance analysis
basis 6-31g
scftype rhf
runtype gradient
vectors atoms
enter 1
The above is for 6-31G calculation of any neutral molecule.
[NOTE: For more examples look at test/c28test/cquantumtest/]
For complete information about GAMESS input see the CFS web site
http://www.dl.ac.uk/CFS.
For further information and updates on CHARMM/GAMESS-UK interface
see http://www.cse.clrc.ac.uk/qcg/chmguk
==========================================================
Top
Installation
------------
Installation itself cannot be fully automated yet so one has to
follow this procedure (if there are any problems ask p.sherwood@dl.ac.uk):
1. Unpack the GAMESS-UK distribution as a subdirectory of gukint:
source/gukint/GAMESS-UK
2. install.com <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 not 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
gnu mpich OK
Compaq alpha - OK
Porting Notes
-------------
It is necessary to ensure that charmm_configure processes
the GAMESS-UK Makefiles 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 which complicates the charmm_configure script.
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 some platforms the Global Array port of GAMESS-UK
can be used, but this is not supported yet by the standard
distribution. See the web site http://www.cse.clrc.ac.uk/Activity/CHMGMS
for more details of the current status.
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 install.com, set the environment variables
MPI_LIB - the directory holding libmpi.a (or similar)
MPI_INCLUDE - the directory holding mpif.h (etc)
you may also need to edit GAMESS-UK/m4/Makefile.in as these
directories are specified for most platforms.
- Some changes may be needed to build/UNX/Makefile_<arch> to support
loading with the parallel libraries (e.g. using MPILD)
==========================================================
Installation
------------
Installation itself cannot be fully automated yet so one has to
follow this procedure (if there are any problems ask p.sherwood@dl.ac.uk):
1. Unpack the GAMESS-UK distribution as a subdirectory of gukint:
source/gukint/GAMESS-UK
2. install.com <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 not 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
gnu mpich OK
Compaq alpha - OK
Porting Notes
-------------
It is necessary to ensure that charmm_configure processes
the GAMESS-UK Makefiles 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 which complicates the charmm_configure script.
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 some platforms the Global Array port of GAMESS-UK
can be used, but this is not supported yet by the standard
distribution. See the web site http://www.cse.clrc.ac.uk/Activity/CHMGMS
for more details of the current status.
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 install.com, set the environment variables
MPI_LIB - the directory holding libmpi.a (or similar)
MPI_INCLUDE - the directory holding mpif.h (etc)
you may also need to edit GAMESS-UK/m4/Makefile.in as these
directories are specified for most platforms.
- Some changes may be needed to build/UNX/Makefile_<arch> to support
loading with the parallel libraries (e.g. using MPILD)
==========================================================
Top
GAMESS-UK/CHARMM interface status (July 2000)
- Parallel version is functional, but for most platforms it
will require changes to install.com Makefile_$chmhost
and/or charmm_configure to activate
- All CHARMM testcases are still OK when CHARMM is compiled
with GAMESS-UK inside.
- GAMESS, GAMESSUK, CADPAC and QUANTUM keywords cannot coexist
in pref.dat
- GAMESS-UK recognizes atoms by their masses as specified in the
RTF file
GAMESS-UK/CHARMM interface status (July 2000)
- Parallel version is functional, but for most platforms it
will require changes to install.com Makefile_$chmhost
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