CHARMM c36b1 mscale.doc
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Multi Scale Command: MSCALE
The multiscale command causes CHARMM to run several
independent but connected calculations using subsystems. The
calculations can use either CHARMM or other programs with a consistent
interface.
by Milan Hodoscek and Bernard Brooks
* Menu:
* Syntax:: Syntax of the mscale specification
* Examples:: Examples to run the MSCAle command
* Notes:: Notes abot the MSCAle command
File: Mscale -=- Node: Syntax
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[SYNTAX MSCAle]
Main script commands:
MSCAle [ NSUBsystems integer ]
SUBSystem keyname [ PROGram filename ] [ CRYStal ] [ ATOM ] -
[ AMBEr ] [ TORQue ] -
[ NPROC integer ] [ FNPR integer ] -
[ COEFf real ] [ LAMBda ] [ MLAMbda ] -
[ INPUt filename ] [ OUTPut filename ] atom-selection
SYSDisplay
END
Subsystem commands:
SERVer [ NCALls integer ] [ ATOM ] [ CRYStal ] [ TORQue ] [ DEBUg ]
Meaning of individual keywords:
SUBSystem - Create a new subsystem
NSUBS - the number of SUBSystems to be setup
keyname - Always read but currently not used for further usage in the
code. Must follow immediately the SUBSystem keyword.
This is the name of the subsystem.
COEFf real - coefficient with which to scale the energy/forces
of this subsystem
LAMBda - Also scale by PERT's lambda value
MLAMbda - Also scale by PERT's 1-lambda value
ATOM - Flag to decide on communication of atom data:
number of atoms in this subsystem and their atomic
numbers in floating point format
NPROC - How many processes this subsystem will use. eg
semipempirical methods 1, since they are not
parallel, but ab initio and some MM methods can use
parallel here.
FNPRoc - Forward this number to the program which is run
through the interface in CALL SYSTEM(). Only works
with ATOM flag!
AMBEr - Specify that the specified program is a SANDER executable
from AMBER. This option calls the PROGram with the
"-server" command line argument, which is needed to start
SANDER as an MSCALE server.
The folowing 3 keywords must be specified. There are no defaults for them!
PROGram - the filename of the program to execute for this subsystem
INPUt - the filename of the script to run on the subsystem
OUTPut - the filename of the output from the program
CRYStal - communicate the crystal type (CUBIc, RHDO, etc.), unit cell
data, and the virial. This option must be specified in both
the SUBSystem and SERVer commands.
TORQue - indicates that the 3x3 rotation matrix of any defined torque
centers (see torque.doc) within the atom-selection is to
be passed via MSCALe to the slaves andf the 1x3 torque vector
is to be returned to the master process. This option must be
specified in both the SUBSystem and SERVer commands.
SYSDisplay - Display the info about the whole setup
END - Must be specified to end the MSCAle block.
SERVer - Put CHARMM in server mode.
NCALLs integer - Number of energy calls in server mode before going
to next CHARMM command in the server script.
If the number is not specified, the command will
run until the client terminates.
DEBUg - Makes the server print out the results of each energy evaluation
that it performs. This option is useful for debugging, but
probably should not be used for long runs (it will produce too
much output).
As of c36a1 MSCAle now supports normal mode (i.e. second derivatives) at both
the all-atom and hybrid QM/MM levels of theory. Both analytic and finite
difference 2nd derivatives are supported. To activate the finite difference
2nd derivatives use the following SERVer command (see vibran_mscale, vsys1.inp,
or vsys2.inp in c35test)...
SERVer finite step 0.005
where 0.005 is the step size used during the finite difference calculation.
File: Mscale -=- Node: Examples
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EXAMPLE 1: Typical input for substraction method (ONIOM):
Main script:
READ/GENERATE PSF
READ PARAM
READ COOR
MSCAle NSUBs 2
SUBSystem high coef 1.0 program "charmm" input "sub1.inp" -
output "sub1.out" sele resid 4 end
SUBSystem low coef -1.0 program "charmm" input "sub2.inp" -
output "sub2.out" sele resid 4 end
END
DYNA ....
Subsystem 1 (sub1.inp)
READ/GENERATE PSF for one residue
READ PARAM (one kind of parameters)
READ COOR
NBONDS
SERVER
Subsystem 2 (sub2.inp)
READ/GENERATE PSF for one residue
READ PARAM (different kind of parameters than in one)
READ COOR
NBONDS
SERVER
File: Mscale -=- Node: Notes
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Miscellaneous Notes:
I.
To dynamically start new processes in parallel MPI-2 standard is used,
namely MPI_COMM_SPAWN routine. It is availalble in OpenMPI library
(currently in use) and MPICH-2. MPICH-2 has some problems with
standard I/O so it is not recommended for use as of June 2007.
As of April 2009 the recommended command to compile CHARMM is the
following:
install.com gnu xxlarge x86_64 M +REPDSTR +MSCALE +ASYNC_PME +ALTIX_MPI +GENCOMM
II.
Matrices for coefficients in substraction methods:
L=low level theory, H=high level theory
B=big system, S=small system
B S
L 1 -1
H 0 1
If you have 3 levels:L, M, H, and 3 reagions B, M, S: B > M > S!
B M S
L 1 -1 0
M 0 1 -1
H 0 0 1
III.
How to do the additive methods ?
File: Mscale -=- Node: Interfaces
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MSCAle Interfaces contributed by: H. Lee Woodcock (hlwood-at-nih-dot-gov), Benjamin T. Miller (btmiller-at-nhlbi-dot-nih-dot-gov), Joseph D. Larkin (larkinj3-at-nhlbi-dot-nih-dot-gov), and Milan Hodoscek (milan-at-cmm-dot-ki-dot-si). Currently four (4) external QM programs are interfaced to CHARMM via the MSCAle command. These programs are in addition to the currently supported QM packages that are interfaced with CHARMM (GAMESS, GAMESS-UK, Q-Chem, SCC-DFTB, ect.). 1. NWChem (http://www.emsl.pnl.gov/docs/nwchem/nwchem.html) 2. MOLPRO (http://www.molpro.net/) 3. PSI 3 (http://www.psicode.org/) License:(GPL) 4. GAUSSIAN 03 (http://www.gaussian.com/) Support for additional QM packages is underway and will be added in the future. To request support for a particular package please contact H. Lee Woodcock, Joseph D. Larkin, or Milan Hodoscek. Below are examples of how to run the various QM packages via MSCAle. All packages require a control file that dictates the options to be passed to the individual package. ----------------------------------------------------------------------------- 1. NWChem: Here is an example of control file that is needed for a NWChem calculation... title "for interface" basis "ao basis" * library "6-31g*" end geometry noautosym end task dft gradient task shell "/bin/rm -f sys1.b sys1.b^-1 sys1.c sys1.db" task shell "/bin/rm -f sys1.gridpts.0 sys1.grinfo.0" task shell "/bin/rm -f sys1.movecs sys1.p sys1.zmat" ----------------------------------------------------------------------------- 2. MOLPRO: Here is an example of control file that is needed for a MOLPRO calculation... ***Title memory,1,m SET,CHARGE=0 BASIS=sto-3g thresh,energy=1.d-10 hf optg,maxit=0,coord=cart,startcmd=hf ----------------------------------------------------------------------------- This file will perform a single SCF analytic gradient calculation. If a method that does not support analytic gradients (i.e. CCSD(T)) is desired the "optg" line must be changed to read like the following line: optg,numerical,maxit=0,coord=cart,displace=cart,startcmd=hf The correct geometry section will be written with the correct keywords immediately following the line containing the "memory" specification. ----------------------------------------------------------------------------- 3. PSI 3: Here is an example of control file that is needed for a PSI 3 calculation... psi: ( label = "Title" no_reorient=true subgroup=c1 jobtype = sp wfn = scf reference = rhf dertype = first basis = "STO-3G" geometry = ( ) ) In this case the "no_reorient" keyword must be used to keep all forces in the correct reference frame. The current molecular geometry will be placed automatically in the "geometry" section. ----------------------------------------------------------------------------- 4. Gaussian 03: Here is an example of control file that is needed for a G03 calculation... %mem=100MB %NProcShared=2 %NProcLinda=4 #HF/sto-3g FORCE NOSYMM ***user specified title 0 1 ----------------------------------------------------------------------------- Here it should be noted the last line in the control file should be the spin and multiplicity specifications. i.e. there should be no blank line at the end of this control file as there is in a typical gaussian input file as the current geometry will be appended and the final blank line inserted afterwards. Additionally, interfaces have been developed to the SANDER program (part of the AMBER package) and to the TINKER program. Please contact Benjamin T. Miller for further information about these interfaces.
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