[gmx-users] WHAM with multiple force constants

Jochen Hub jochen at xray.bmc.uu.se
Sat Feb 19 00:23:02 CET 2011

On 2/10/11 Feb 10,6:08 AM, jkhao at 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!).



> 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.
> ----------------------------------------------------------------------
> Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs-mrs.fr).

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

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