[gmx-users] pbc atom

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 24 17:11:30 CEST 2010

chris.neale at utoronto.ca wrote:
> I have seen this before, and there are a few possible reasons, but I'm 
> still waiting to see that histogram with two peaks 
> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). 
> It's really hard to help you when we have to guess what the problem 
> looks like... or perhaps you posted it and I missed it?

The histogram was posted several days ago:


The attachment link is:



> -- original message --
> O.K thanks anyway
> Justin A. Lemkul 
> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>> Gavin Melaugh wrote:
>>> Thanks Justin
>>> Have you any idea why when generating umbrella histograms for the pmf I
>>> would get two peaks in the histograms above a distance of 2 nm, but
>>> below 2 nm I get well behaved histograms that lead to a very
>>> good profile in the pmf. To the best of my knowledge the configurations
>>> are all very well equilibrated at their respective COM distances.
>>> Umbrella sampling is performed on all windows using a force constant of
>>> 1000 kj/mol at 600 K.
>> Sorry, no clue.


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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