VMD-L Mailing List

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Mon Jan 15 2007 - 17:30:44 CST

Hi,
 
I wrote the attached script for replica exchange simulations because I thought it would be useful for me and I couldn't spot something that would do the same thing in the script library. Please feel free to evaluate it, improve on it and put it in the library if you think it would be useful. Do let me know if you find something seriously wrong with it!!!
 
REQUIREMENTS: VMD Version 1.8.5 (I didn't test it for other versions!)

DESCRIPTION:
REselectByTemp.tcl takes the various dcds output from a Replica Exchange simulation and loads the dcds by temperature (not by replica).
It is prepared to function with parm7 *top files, not with psf files, but it can be easily modified to work with *psf files.
This script requires that a *conf file exists in the directory above it, because some variables are defined there (see file *.conf given in the example provided in NAMD for the replica exchange simulations)
This script will not work properly if of the target temperatures is bigger than the number of steps contained in the first dcd frame (to avoid problems, each dcd frame should be composed of 1000 steps at least, because it is unlikely that simulations at T larger than 1000 will be performed.
This script will not work properly if replica 1 does not experience all possible temperatures (as all replicas should in a replica exchange simulation)

EXAMPLE USAGE
To run, put this script in the same directory as the *dcd and *dat files output by the RE simulation, in a Linux machine that runs VMD. Open it and define the name of the relevant *targtemp.dat and *conf files. Then type at the prompt
 
 vmd -e REselectByTemp.tcl

Best,
 
Ana
 
_________________________________
Ana Célia Araújo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
USA
 
 <http://www.gfct.fisica.uminho.pt/Members/acvv>
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846
avilaverde_at_engr.psu.edu
http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
http://www.gfct.fisica.uminho.pt/Members/acvv
_________________________________