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hlamcrex.pl
Usage
usage: hlamcrex.pl [options] [files]
options: [-n runs]
[-f listfile]
[-par initruns=value,equilruns=value,
[no]save,savebestfreq=value,
natpdb=file,seq=file]
[-mcpar mcruns=value,mode=coupled|free,
[no]keepchain,[no]eval,
caforce=value,hmcmforce=force]
[-latpar icycle=val,ncycle=value,
stiff=val,short=val,central=val,kdcore=val]
[-latopt gridsize=value]
[-aapar CHARMMparams]
[-evalpar CHARMMparams]
[-temp nwin:min:max]
[-ltemp min:max]
[-condfile file]
[-dir workdir]
[-ens tag] [-ensdir dir]
[PARALLELoptions]
[-log file] [-aalog file] [-evallog file]
Description
This utility is used for running replica exchange hybrid lattice/all-atom simulations.
A detailed explanation of the methodology is found in the documentation for
the version for single runs, hlamc.pl.
The options -latpar, -aapar, and -evalpar
for the lattice and all-atom modeling parts are the same as in
hlamc.pl. Hybrid Monte Carlo options are given
with -mcpar. Additional options for replica exchange sampling
are very similar to the corresponding options in aarex.pl.
In addition to the temperatures used in the replica exchange Metropolis
criteria the hybrid method also requires corresponding temperatures for the
lattice simulations. The lattice run temperatures are given with -ltemp
or through a condition file with -condfile.
Options
- -help
- usage information
- -n runs
- number of replica exchange cycles
- -par key=value[,...]
- replica exchange simulation paramters
- -mcpar key=value[,...]
- multi-scale Monte Carlo simulation parameters
- -latpar key=value[,...]
- MONSSTER simulation parameters
- -latopt key=value[,...]
- additional options for MONSSTER chain generation
- -aapar key=value[,...]
- CHARMM simulation parameters
- -evalpar key=value[,...]
- CHARMM energy evaluation parameters
- -temp nwin:min&#max
- number and range of temperature replicas
- -ltemp min:max
- MONSSTER simulation temperature range
- -condfile file
- condition file
- -dir directory
- data directory
- -ens tag
- ensemble tag for storing conformations from lowest temperature replica
- -ensdir dir
- ensemble directory
- -log file
- output log file
- -aalog file
- CHARMM log file
- -evallog file
- CHARMM energy evaluation log file
Examples
hlamcrex.pl -n 5 -dir data -par seq=1vii.seq -mcpar mcruns=5,mode=free,noeval -latpar ncycle=2 -aapar dielec=rdie,epsilon=4.0,sdsteps=20,minsteps=100 -temp 4:30:40 -ltemp 1.0:1.5 -aalog aa.log -log server.log 1vii.sample.{1,2,3,4}.pdb
runs a hybrid lattice/all-atom replica exchange simulation with four temperature windows.