[gmx-users] Weird result of WHAM

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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