On 2/10/11 Feb 10,6:08 AM, jk...@ifr88.cnrs-mrs.fr wrote:
Hi,
I'm running an Umbrella Sampling analysis, with 1A steps in the
reaction coordinate (distance) to estimate a PMF. However, owing to
(high?) energetic barriers between my two proteins, some coordinates
are not sampled. I intend to run simulations with stronger force
constants to prevent my protein from fleeing to the nearest energetic
minima.
So my question is : does using different force constants to restrain
the distance between my two proteins influences the PMF estimated by
g_wham ?
No, it is perfectly fine (and sometimes necessary) to combine umbrella
simulations with different force constants. The g_wham result should be
fine (if not, tell me, thanks!).
Cheers,
Jochen
From what I understood, it doesn't seems so, as long as the
distributions are well overlapped. But since I intend to invest a
considerable amount of CPU time, a confirmation would be really
apreciated !
Thanks,
Jonathan.
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Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs-mrs.fr).
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Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell& Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
http://xray.bmc.uu.se/~jochen/index.html
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