[gmx-users] REMD As A Function of Distance Between 2 Chains

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 15 07:57:31 CET 2007

Mark Abraham wrote:
> Huey Ling Tan wrote:
>> Dear all ,
>> thank you for those comments, we are aware of the paper.  However, we 
>> are not sure how to implement the replica exchange in gromacs.  We 
>> would like to run a set of replicas in which each replica corresponds 
>> to a different set of umbrella parameters.  However, when setting up a 
>> replica exchange run, all .tpr files use the same .ppa file so that 
>> each replica will have the same umbrella potential parameters.   Do 
>> you know how to get around this problem.
> You will have to change the code to implement this algorithm.'
But first check the pull code in the cvs version of gromacs, where all 
options have been moved to the mdp file.

> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list