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]

Show source

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.