[gmx-users] umbrella sampling (PMF) position discrepancy

Justin Lemkul jalemkul at vt.edu
Tue Sep 11 03:38:48 CEST 2012

On 9/10/12 9:30 PM, Jianguo Li wrote:
> I guess is that g_wham takes the distance from tpr file which calculates the distance using grommp.
> It seems that the distances calculated using g_dist and grompp are different, as discussed in this forum about 10 days ago.

This is a fairly frequent complaint, but I have never encountered it myself in 
my own usage.  Perhaps it is very situation-dependent, if there is indeed an 
issue to be fixed.  If Raphael wants me to look into the issue, please send me 
(off-list) a coordinate file, .tpr file, and any .ndx and .mdp files necessary 
to reproduce this issue.  I will try to have a look and see if I can uncover 
what might be going on.



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


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