[gmx-users] Weird result of WHAM

Justin Lemkul jalemkul at vt.edu
Wed Nov 14 19:40:33 CET 2012

On 11/14/12 8:43 AM, Netaly Khazanov wrote:
> Dear All,
> I've performed TMD simulation using NAMD program from the state A to B, and
> visa versa from the state B to A.
> Umbrella sampling calculations were done on the snapshots that were  taken
> from the path ( A to B & B to A) by using Gromacs.
> Afterwards WHAM analysis was calculated in order to extract PMF plot.
> However the result of  ΔG of PMF plot  in the case of A to B path was the
> opposite (for example -10)  than in the case of B to A ( 10). ( I would
> expect to get the same result in both cases).

Can you explain in greater detail what states A and B correspond to?  I would 
expect the opposite - the reverse of a process should have the same magnitude of 
deltaG and opposite sign (i.e. ligand binding/unbinding).

> By merging the data of both paths, WHAM gives result of   ΔG=-10.
> The result is very not consistence. I'm  probably missing something.

You'll have to be more explicit about what you're doing, i.e. actual commands, 
input, and output.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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