g09 (c47b1)
Combined Quantum Mechanical and Molecular Mechanics Method
Based on Gaussian09 in CHARMM
G. Hou, J. Zienau, and Q. Cui
(cui@chem.wisc.edu)
based on the Q-Chem interface by Lee Woodcock
Ab initio program Gaussian09 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).
The interface currently provides basic functionality for QM/MM calculations
of energy & gradient. It can also be used in conjunction with the
Solvent Macromolecule Boundary Potential (SMBP; » pbeq )
* Description | Description of the GAUS commands.
* Usage | How to run Gaussian09 in CHARMM.
Based on Gaussian09 in CHARMM
G. Hou, J. Zienau, and Q. Cui
(cui@chem.wisc.edu)
based on the Q-Chem interface by Lee Woodcock
Ab initio program Gaussian09 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).
The interface currently provides basic functionality for QM/MM calculations
of energy & gradient. It can also be used in conjunction with the
Solvent Macromolecule Boundary Potential (SMBP; » pbeq )
* Description | Description of the GAUS commands.
* Usage | How to run Gaussian09 in CHARMM.
Top
The Gaussian09 QM potential is initialized with the GAUS command.
[SYNTAX GAUS]
GAUS [REMOve] [EXGRoup] [DIV] (atom selection)
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
DIV: Charge on MM link host atom divided equally among
other MM atoms in the same group.
The NOGUess option (» qchem ) is always implied!
Example:
ENVI g09exe "/share/apps/gaussian/g09/g09"
ENVI g09fchk "/share/apps/gaussian/g09/formchk"
ENVI g09cmd "G09CMD"
ENVI g09profile "G09PROFILE"
ENVI g09inp "g1"
GAUS nogu remove sele QM end
The Gaussian09 QM potential is initialized with the GAUS command.
[SYNTAX GAUS]
GAUS [REMOve] [EXGRoup] [DIV] (atom selection)
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
DIV: Charge on MM link host atom divided equally among
other MM atoms in the same group.
The NOGUess option (» qchem ) is always implied!
Example:
ENVI g09exe "/share/apps/gaussian/g09/g09"
ENVI g09fchk "/share/apps/gaussian/g09/formchk"
ENVI g09cmd "G09CMD"
ENVI g09profile "G09PROFILE"
ENVI g09inp "g1"
GAUS nogu remove sele QM end
Top
commands and the GAUS command itself. The Gaussian parameters are specified
in an additional file as defined by the G09CMD environment variable. The
environment section in the CHARMM input defines the Gaussian program location,
the parameter filenames as well as the input/output filenames and scratch
directory:
Use of ENVIronment commands in the CHARMM input file:
ENVI G09EXE "/share/apps/gaussian/g09/g09"
ENVI G09FCHK "/share/apps/gaussian/g09/formchk"
ENVI G09CMD "G09CMD"
ENVI G09PROFILE "G09PROFILE"
ENVI G09INP "g1"
ENVI GAUSS_SCRDIR "/scratch/"
1. G09EXE and G09FCHK point to the Gaussian as well as the formchk executable
2. G09CMD specifies the file that provides the calculation parameters (see below)
3. G09PROFILE is a shell input file that can be used to source additional
env variables that might be needed for Gaussian; usually, however, an
empty file will do (but it has to be provided)
4. G09INP provides the name of the input/output files. For example, "g1"
will produce g1.inp and g1.log. The input file is automatically generated
by the interface
5. GAUSS_SCRDIR points to the scratch file; it might be more useful to
define this in the submission (pbs) script
Gaussian parameter file G09CMD
------------------------------
The structure is evident in the following example for a
B3LYP/6-31G* calculation of a neutral molecule. The $pop
section allows to provide options for population analysis
(e.g., calculation of Merz-Kollman ESP charges by specifying
"pop=mk" beneath the $pop keyword), $extra allows for general
additional options to Gaussian, and $nproc specifies the
number of processors Gaussian should use.
$extend can be used for including extra lines at the end of the
generated Gaussian input file (for example, for specifying the
radius of element(s) when "pop=(mk,readradii)" needs to be used).
It should be noted that the $extend section should be the LAST
section in the G09CMD file since everything after the $extend
keyword is assumed to belong to this section. Also, blank lines
between entries in the $extend section are allowed but the line
immediately following the line containing $extend should not be
a blank line if the $extend section has any entries at all.
-----------------------------------------------------------
$method
b3lyp
$basis
6-31g(d)
$title
test input for g09
$charge
$spin
$pop
$extra
$nproc
$mem
1000MB
$extend
-----------------------------------------------------------
commands and the GAUS command itself. The Gaussian parameters are specified
in an additional file as defined by the G09CMD environment variable. The
environment section in the CHARMM input defines the Gaussian program location,
the parameter filenames as well as the input/output filenames and scratch
directory:
Use of ENVIronment commands in the CHARMM input file:
ENVI G09EXE "/share/apps/gaussian/g09/g09"
ENVI G09FCHK "/share/apps/gaussian/g09/formchk"
ENVI G09CMD "G09CMD"
ENVI G09PROFILE "G09PROFILE"
ENVI G09INP "g1"
ENVI GAUSS_SCRDIR "/scratch/"
1. G09EXE and G09FCHK point to the Gaussian as well as the formchk executable
2. G09CMD specifies the file that provides the calculation parameters (see below)
3. G09PROFILE is a shell input file that can be used to source additional
env variables that might be needed for Gaussian; usually, however, an
empty file will do (but it has to be provided)
4. G09INP provides the name of the input/output files. For example, "g1"
will produce g1.inp and g1.log. The input file is automatically generated
by the interface
5. GAUSS_SCRDIR points to the scratch file; it might be more useful to
define this in the submission (pbs) script
Gaussian parameter file G09CMD
------------------------------
The structure is evident in the following example for a
B3LYP/6-31G* calculation of a neutral molecule. The $pop
section allows to provide options for population analysis
(e.g., calculation of Merz-Kollman ESP charges by specifying
"pop=mk" beneath the $pop keyword), $extra allows for general
additional options to Gaussian, and $nproc specifies the
number of processors Gaussian should use.
$extend can be used for including extra lines at the end of the
generated Gaussian input file (for example, for specifying the
radius of element(s) when "pop=(mk,readradii)" needs to be used).
It should be noted that the $extend section should be the LAST
section in the G09CMD file since everything after the $extend
keyword is assumed to belong to this section. Also, blank lines
between entries in the $extend section are allowed but the line
immediately following the line containing $extend should not be
a blank line if the $extend section has any entries at all.
-----------------------------------------------------------
$method
b3lyp
$basis
6-31g(d)
$title
test input for g09
$charge
$spin
$pop
$extra
$nproc
$mem
1000MB
$extend
-----------------------------------------------------------