[gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 28 14:42:42 CEST 2009

Stefan Hoorman wrote:

> To generate each window I use "trjconv -f 
> original_separation_trajectory.xtc -s topol.tpr -dump 
> time_where_specific_distance_is_found -o 
> frame_where_separation_between_structures_is_x.gro"
> Once I have the coordinate files regarding this specific distance 
> between my pull groups, I simulate each of them (using the same 
> topol.top file, index.ndx...etc) but with the new md_pull.mdp file I've 
> shown here earlier.
> Is this wrong for wham analysis?

This should be right, hence my confusion about the histogram.  Are you sure 
there's only one peak?  Have you looked at it with a text editor?  There should 
be multiple entries in the file, one for each window that you're simulating?


> Thank you
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list