aarexAmber.pl Show Source
aarexAmber.pl [options] [files]
options: [-n runs]
[-par initruns=value,equilruns=value,
  [no]save,savebestfreq=value,archive
  ensmode=add|replace,natpdb=file,partop=file
[-temp nwin:min:max]
[-condfile file]
[-f listfile]
[-mdpar AmberParams]
[-mdopt [no]trajout,[no]conslim,
  limforce=value,limsel=ca|cb|cab|heavy],
  [no]translate,ambercoor
[-l refPDB min:max[=min:max ...]]
[-cons [ca|cb|cab|heavy] ref|self min:max[_force][=...]]
[-opt optionsfile]
[-dir workdir]
[-ens tag] [-ensdir dir]
[PARALLELoptions]
[-log file] [-elog file] [-amberlog file]

This script works very similar to aarex.pl. It adds replica exchange functionality to Amber.

Server.pm  ReXServer.pm  AmberReXServer.pm  Client.pm  ReXClient.pm  GenUtil.pm  Molecule.pm  Ensemble.pm  Amber.pm
Michael Feig, Brooks group, TSRI
John Karanicolas, Brooks group, TSRI