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
--
========================================
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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