[gmx-users] pmf_calculation

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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