chris.ne...@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:
http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
The attachment link is:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
-Justin
-- 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
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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