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, 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

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.