On Feb 10, 2011, at 3:08 PM, 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 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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