Re: [AMBER] Wham tolerance

From: Adrian Roitberg <>
Date: Mon, 18 Nov 2013 16:41:16 -0500

Are you absolutely positive that your umbrella windows are overlapping ?
The behavior you describe sometime is associated with bad choice of
windows or force constants, which gives unconverged (and they can never
convergre) surfaces.


On 11/18/13 4:38 PM, Fabrício Bracht wrote:
> Hello. I am not sure if this is the correct place to place this question,
> since it is only partially related to amber, so excuse me if it is not. I
> am analyzing the free energy path of a proton transfer. For this I am using
> DFTB/Umbrella sampling and steps of 0.1 Angstrom. When using the Alan
> Grossfield's WHAM, I have noticed that the tolerance value used in the
> analysis changes the relative free energy values obtained. For instance, if
> I use tolerance of 0.01 I get a free energy difference between reactant and
> product of 6.53 kcal/mol, if I use tol value of 0.001 I get a delta of 7.00
> kcal/mol. For tol 0.0001, I get 7.05, etc. The WHAM manual states that if
> the free energy curves have stopped changing, your tolerance is small
> enough. In that case, the smaller the tolerance change the smaller the
> changes on the values. But, as far as I've tested, it never stops changing.
> It does so in increasingly smaller fractions of the free energy values.
> I guess my question is: When to stop?
> Thank you
> Fabrício
> _______________________________________________
> AMBER mailing list

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
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Received on Mon Nov 18 2013 - 14:00:03 PST
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