Yes. They are overlapping. The force constant is the lowest that allowed me
to properly sample high energy regions. The differences in the free energy
values I get with the different tol values are proportional to the amounts
of zeros that I use for tol. For example:
Tol Value at 0.584444 Angstrom
0.01 6.559799
0.001 7.006187
0.0001 7.051056
0.00001 7.055565
0.000001 7.056019
0.0000001 7.056064
0.00000001 7.056069
0.000000001 7.056069
Is this normal?
Fabrício
2013/11/18 Adrian Roitberg <roitberg.ufl.edu>
> 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.
>
> adrain
>
> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 18 2013 - 14:30:02 PST
