[gmx-users] PMF of helix dimer

Ragnarok sdf fabracht1 at gmail.com
Sat Sep 19 22:48:01 CEST 2009

I am performing PMF calculations for my helix dimer using umbrella potential
and WHAM analysis. I have already obtained the main reaction coordinates and
have divided my path into several windows. From each of this windows,
corresponding to a specified distance between my two dimers, I am simulating
400 ps in order to obtain the entry files for g_wham. I have observed,
although, that my structures do not stay within the specified distance. The
two monomers fall back onto each other, as one would expect happening. I
have read that this sampling windows must be in equilibrium, i.e., both
monomers should remain where they are in order to get a good overlap between
windows. Will that be a problem later on when I try to do my wham analysis?
Thank you
Fabrício Bracht
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