nwchem (c44b1)
Combined Quantum Mechanical and Molecular Mechanics Method
Based on NWChem in CHARMM
by Milan Hodoscek
July 2017
(milan@cmm.ki.si, hmilan@gmail.com)
Ab initio program NWChem (http://www.nwchem-sw.org) is
connected to CHARMM program in a QM/MM method. The implementation is
based on the gukini.src source file which already works for other ab
initio programs interfaced to CHARMM. Since this is more than 2 decades
later than the first ab initio program interfaced to CHARMM (GAMESS in
1993) some of the strategies are much cleaner and more easy to
maintain for NWChem program interface than for others. Since both
programs, NWCHem and CHARMM are linked into a single executable, we
need to protect NWCHem library calls in CHARMM by #if KEY_NWCHEM==1,
because the routines are not available when there are no NWChem
libraries installed on a machine.
* Description | Description of the NWCHem commands.
* Using | How to run NWChem in CHARMM.
* Replica path | How to run NWChem/CHARMM with REPLICA/PATH.
* Installation | How to install NWChem in CHARMM environment.
* Status | Status of the interface code.
* Functionality | Functionality of the interface code.
* Implementation | Implementation.
Based on NWChem in CHARMM
by Milan Hodoscek
July 2017
(milan@cmm.ki.si, hmilan@gmail.com)
Ab initio program NWChem (http://www.nwchem-sw.org) is
connected to CHARMM program in a QM/MM method. The implementation is
based on the gukini.src source file which already works for other ab
initio programs interfaced to CHARMM. Since this is more than 2 decades
later than the first ab initio program interfaced to CHARMM (GAMESS in
1993) some of the strategies are much cleaner and more easy to
maintain for NWChem program interface than for others. Since both
programs, NWCHem and CHARMM are linked into a single executable, we
need to protect NWCHem library calls in CHARMM by #if KEY_NWCHEM==1,
because the routines are not available when there are no NWChem
libraries installed on a machine.
* Description | Description of the NWCHem commands.
* Using | How to run NWChem in CHARMM.
* Replica path | How to run NWChem/CHARMM with REPLICA/PATH.
* Installation | How to install NWChem in CHARMM environment.
* Status | Status of the interface code.
* Functionality | Functionality of the interface code.
* Implementation | Implementation.
Top
The NWChem QM potential is initialized with the NWCHem command.
[SYNTAX NWCHem]
NWCHem [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.
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(8? check) 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/cquantum/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.
If you see the following error in your output script:
FNIDEL> Cannot find element type for number....
That means you either have wrong order in the ADDLink command or the atom
that should be MM is in the QM selection.
=======================================================================
The NWChem QM potential is initialized with the NWCHem command.
[SYNTAX NWCHem]
NWCHem [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.
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(8? check) 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/cquantum/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.
If you see the following error in your output script:
FNIDEL> Cannot find element type for number....
That means you either have wrong order in the ADDLink command or the atom
that should be MM is in the QM selection.
=======================================================================
Top
In order to run NWChem and CHARMM on parallel machines I/O of
NWChem 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 NWCHem command itself. NWChem commands are in a
separate file which is pointed to by NWCHEM_INPUT environment variable.
Names of the files for NWChem are specefied with environment
variables as follows:
use ENVIronment command inside CHARMM
envi NWCHEM_INPUT "nwchem.nw" ! quotes needed for lowercase names
envi NWCHEM_OUTPUT "nwchem.out"
envi NWCHEM_RTDB "ala.db"
For complete information about NWChem input see the
documentation file in NWChem distribution.
Example:
--------
NWChem commands have to be in a separate file. Example for the NWChem input
follows:
----------------------------------------------------------------------------
title "the interface with charmm"
# this input is because we don't want to parse
# QM stuff in CHARMM
# this name must match the envi command in CHARMM script:
# envi NWCHEM_RTDB "ala.db"
start ala
basis
* library sto-3g
end
# anything goes here, but for practical reasons one
# should make an atom (or more) with the same multiplicity & charge
# as a QM region
geometry noautosym
Li 0 0 0
end
charge -1
#scf
#singlet
#uhf
#end
#dft
#xc b3lyp
#end
# We use the same task for real QM/MM run
task scf gradient
----------------------------------------------------------------------------
The above is for STO-3G calculation of a charged QM region. Geometry
block cannot be empty, but it can contain as few as possible atoms.
However keeping the original NWChem input scripting allows for
independent development of both programs, and it is easy to work with
the new features of NWChem within CHARMM interface, without additional
devlopment in the interface code in the CHARMM program.
[NOTE: For more examples look at test/cquantum/nwchemtst.inp]
==========================================================
In order to run NWChem and CHARMM on parallel machines I/O of
NWChem 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 NWCHem command itself. NWChem commands are in a
separate file which is pointed to by NWCHEM_INPUT environment variable.
Names of the files for NWChem are specefied with environment
variables as follows:
use ENVIronment command inside CHARMM
envi NWCHEM_INPUT "nwchem.nw" ! quotes needed for lowercase names
envi NWCHEM_OUTPUT "nwchem.out"
envi NWCHEM_RTDB "ala.db"
For complete information about NWChem input see the
documentation file in NWChem distribution.
Example:
--------
NWChem commands have to be in a separate file. Example for the NWChem input
follows:
----------------------------------------------------------------------------
title "the interface with charmm"
# this input is because we don't want to parse
# QM stuff in CHARMM
# this name must match the envi command in CHARMM script:
# envi NWCHEM_RTDB "ala.db"
start ala
basis
* library sto-3g
end
# anything goes here, but for practical reasons one
# should make an atom (or more) with the same multiplicity & charge
# as a QM region
geometry noautosym
Li 0 0 0
end
charge -1
#scf
#singlet
#uhf
#end
#dft
#xc b3lyp
#end
# We use the same task for real QM/MM run
task scf gradient
----------------------------------------------------------------------------
The above is for STO-3G calculation of a charged QM region. Geometry
block cannot be empty, but it can contain as few as possible atoms.
However keeping the original NWChem input scripting allows for
independent development of both programs, and it is easy to work with
the new features of NWChem within CHARMM interface, without additional
devlopment in the interface code in the CHARMM program.
[NOTE: For more examples look at test/cquantum/nwchemtst.inp]
==========================================================
Top
Replica/Path method (parallel/parallel setup)
---------------------------------------------
Running NWChem/CHARMM interface with Replica/Path method needs
few additional steps:
- NWChem/CHARMM must be compiled with the parallel
functionality. Make sure that the GENCOMM keyword is in
pref.dat. (Run CHARMM interactively and type pref).
- The number of processes must be equal to number of replicas
multiplied by an integer (1,2,3...). This ensures that each
replica is an independent process. If the factor is more
than 1, it means each replica will run itself in parallel
(parallel/parallel).
- NWChem control file (the one assigned to the INPUT environment
variable) must be linked the number of replica times. Each
symbolic link must have _<int> appended to the original
name:
ln -s test.gms test.gms_1
ln -s test.gms test.gms_2, etc
the number of links must be greater or equal to the number
of replicas
- The path to the above link must be absolute. This depends on
the way CHARMM is run in parallel. For example for MPICH
library one must use the following command:
charmm -p4wd /data/rpath/reaction -p4pg 20cpus < inp > out
The /data/rpath/reaction must be the same on all the
processes, either exact copies or NFS mounted.
- The nwchem output files have also _<int> appended to their names.
Replica/Path method (parallel/parallel setup)
---------------------------------------------
Running NWChem/CHARMM interface with Replica/Path method needs
few additional steps:
- NWChem/CHARMM must be compiled with the parallel
functionality. Make sure that the GENCOMM keyword is in
pref.dat. (Run CHARMM interactively and type pref).
- The number of processes must be equal to number of replicas
multiplied by an integer (1,2,3...). This ensures that each
replica is an independent process. If the factor is more
than 1, it means each replica will run itself in parallel
(parallel/parallel).
- NWChem control file (the one assigned to the INPUT environment
variable) must be linked the number of replica times. Each
symbolic link must have _<int> appended to the original
name:
ln -s test.gms test.gms_1
ln -s test.gms test.gms_2, etc
the number of links must be greater or equal to the number
of replicas
- The path to the above link must be absolute. This depends on
the way CHARMM is run in parallel. For example for MPICH
library one must use the following command:
charmm -p4wd /data/rpath/reaction -p4pg 20cpus < inp > out
The /data/rpath/reaction must be the same on all the
processes, either exact copies or NFS mounted.
- The nwchem output files have also _<int> appended to their names.
Top
Installation
------------
Look at the NWChem home page for instructions how to obtain
and compile the code. Currently it is tested with the following
environment vriables (see the details about the environemnt in the
nwchem web pages):
export LARGE_FILES="TRUE"
export USENOFSCHECK="TRUE"
export NWCHEM_TOP="/home/milan/proj/nwchem/nwchem-6.6"
export NWCHEM_TARGET="LINUX64"
#export NWCHEM_MODULES="all"
export NWCHEM_MODULES="qm"
export USE_MPI="y"
export FC="mpif90"
export F77="mpif77"
Then for CHARMM compilation of ~/c42b1 tree one can use:
export NWCHEM_LIB_CHARMM="/home/milan/proj/nwchem/nwchem-6.6"
mkdir ~/c42b1/build
cd ~/c42b1/build
../configure --nwchem
make -j 8
Installation
------------
Look at the NWChem home page for instructions how to obtain
and compile the code. Currently it is tested with the following
environment vriables (see the details about the environemnt in the
nwchem web pages):
export LARGE_FILES="TRUE"
export USENOFSCHECK="TRUE"
export NWCHEM_TOP="/home/milan/proj/nwchem/nwchem-6.6"
export NWCHEM_TARGET="LINUX64"
#export NWCHEM_MODULES="all"
export NWCHEM_MODULES="qm"
export USE_MPI="y"
export FC="mpif90"
export F77="mpif77"
Then for CHARMM compilation of ~/c42b1 tree one can use:
export NWCHEM_LIB_CHARMM="/home/milan/proj/nwchem/nwchem-6.6"
mkdir ~/c42b1/build
cd ~/c42b1/build
../configure --nwchem
make -j 8