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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, <docmark>hlamc.pl</docmark>.
The options -latpar, -aapar, and -evalpar
for the lattice and all-atom modeling parts are the same as in
<docmarl>hlamc.pl</docmark>. Hybrid Monte Carlo options are given
with -mcpar. Additional options for replica exchange sampling
are very similar to the corresponding options in <docmark>aarex.pl</docmark>.
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
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.