[gmx-users] pmf_calculation

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 5 13:46:49 CEST 2011

shahid nayeem wrote:
> Dear Justin
> I did pmf calculation for my protein-protein complex using your 
> tutorial.Off course changing the pull_direction suitable for my protein 
> but more or less following the same strategy. I am using gromacs_4.5.4 
> and g_wham utility. The profile.xvg file which I get is attached and it 
> shows two dips in PE curve. Please see it and tell me why I am getting 
> these dips.

You have insufficient sampling in at least these two regions.  Your histograms 
should confirm this.



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


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