[gmx-users] WHAM with multiple force constants

XAvier Periole x.periole at rug.nl
Thu Feb 10 15:38:10 CET 2011

On Feb 10, 2011, at 3:08 PM, 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 does not assuming each window is equilibrated.
> 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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