Combined Quantum Mechanical and Molecular Mechanics Method
Based on CADPAC in CHARMM
by Paul Lyne
paul@tammy.harvard.edu
* Menu:
* Description:: Description of the CADPAC commands
* Using:: How to run CADPAC in CHARMM
* Installation:: How to install CADPAC in CHARMM environment
* Status:: Status of the interface code
The CADPAC QM potential is initialized with the CADPac command.
[SYNTAX CADPac]
CADPac [REMOve] [EXGRoup] (atom selection)
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
The syntax of the CADPAC command in CHARMM follows closely that
of the GAMESS command.
For complete information about CADPAC input see Chapter 1 in the CADPAC
distribution.
A QM-MM job using CADPAC needs four input files. The first is the
normal CHARMM input file containing the CADPac command. The second file is
the CADPAC input file specifying the basis set to be used and the Hamiltonian
that is needed. The third and fourth files are libfil.dat and modpot.dat
respectively. These are the library and model potential files that are
supplied with CADPAC.
Cadpac Input File
-----------------
For the CADPAC input file the following cards must be present: TITLE, BASIS,
ATOMS, RUNTYP, START, FINISH.
TITLE: The keyword is always at the start of the input file and is followed
by a one-line title on the next line of the input.
BASIS: This descirbes the basis set to be used for the QM region if a generic
basis set is required. Examples include STO3G,321G,631G,321G*,631G*.
These are the most common. Other basis sets are descibed in the CADPAC
documentation. It is also possible to run a calculation using specific
basis sets for individual atoms. If this feature is required then
the BASIS keyword should be ommitted and the LIBRARY keyword is used
for each atom in the QM region. For a more detailed description of the
library command please refer to the official CADAPC documentation.
All the basis sets that are supported by CADPAC are found in the files
libfil.dat and modpot.dat.
ATOMS: This keyword is always required.
RUNTYP: For the purposes of QM-MM calculations this will either be ENERGY
for a single point calculation or GRADIENT if the forces are also
required. For any minimization or dynamics calculations the GRADIENT
keyword should be used.
START: This keyword is always required.
FINISH: This keyword is always required.
Hamiltonians
------------
The Hamiltonian is HF unless otherwise specified. The Hamiltonian can be
changed by inseerting the appropriate keyword after the RUNTYP key.
For example
MP2 Performs an MP2 calculation
MP3 Performs an MP3 calcualtion
CI Performs a Configuration Interaction calculatio
(please refer to the official CADAPC manual)
For DFT calculations use the KOHNSHAM keyword:
KOHNSHAM LDA MEDIUM GRDWT Performs an LDA calculation with a medium sized
grid for numerical quadrature.
KOHNSHAM BLYP LARGE GRDWT Performs a non-local BLYP calculation with a large
sized grid
For other functionals see the official CADPAC manual.
CADPAC I/O
----------
CADPAC has hard wired units 1,2 and 3 for the libfil.dat, modpot.dat and
cadpac input file so avoid using these elsewhere in the CHARMM stream.
Other units that CADPAC commonly uses for the grid, integrals etc are
13,14,18,35,53,and 54.
Examples
--------
An example of a CADPAC input file to run with CHARMM:
TITLE ! Required
this is a test ! Put whatever you like on one line
BASIS STO3G ! Generic basis set to be used
ATOMS ! Required
GRADIENT ! Run type. Use this for optimizations
START ! Required
FINISH ! Required
The above input file tells CADPAC to use an STO-3G basis for the
atoms in the QM region. CADPAC will perform a gradient evaluation each
time that it is called by CHARMM. If you require just a single point
calculation without gradients just use ENERGY instead of GRADIENT. The input
file above will perform a HF calculation. A DFT calculation is invoked as
follows:
TITLE ! Required
this is a test ! Put whatever you like on one line
BASIS STO3G ! Generic basis set to be used
ATOMS ! Required
GRADIENT ! Run type. Use this for optimizations
KOHNSHAM LDA MEDIUM GRDWT
START ! Required
FINISH ! Required
DF jobs are invoked by the KOHNSHAM card which takes the type of
functional and grid to be used as arguments. In this case an LDA functional is
used. Alternatives include BLYP, B3LYP. For details see the CADPAC
distribution.
A sample shell script to run CHARMM with CADPAC is:
#!/bin/tcsh -f
# parameters:
# 1 data file name
#
echo starting
date
echo $1
set HOME= {where CADPAC data files are}
# data set and output in home directory
#
set data=$HOME/$1.inp
set output=$HOME/$1.out2
# make a temporary directory to hold the workfiles
cd /tmp
mkdir $1
cd $1
# basis set library file assigned to fort.1
# pseudopotential library on fort.2
# the CADPAC input file is copied to UNIT 3
cp $HOME/$1.str fort.3
cp $HOME/$1.par .
cp $HOME/libfil.dat fort.1
#cp $HOME/modpot.dat fort.2
#
# run the program
charmm.exe < $data
rm -r ../$1
An example file can be found in test/c25test/cwat.inp. This
input file also uses cwat.str and the sample run script runcwat.
CADPAC/CHARMM interface status (February 1997) - CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat - CADPAC recognizes atoms by their masses as specified in the RTF file - The program runs on ALPHA, SGI, C90, IBMRS, HPUX platforms. - There are references to a parallel version in the code. This has not been fully tested yet and so won't be included until a future release.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute