MMTSB
Tool Set Documentation

hlamcrex.pl

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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]
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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.