On Mon, Oct 17, 2016 at 5:20 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi everone,
>
> While doing WHAM analysis my free energy keep on changing with tolerance.
>
> When I am using 0.001 tolerance it is 25Kcal/mol
>
> II I am using 0.0001 it is around 35Kcal/mol.
>
>
> I am unable to get which value to trust.
>
May be neither of the energies are trustful due to the convergent issue.
may be you can try:
1. compare PMF 1st and 2nd half of your data
2. check energy histogram overlapping:
http://ambermd.org/tutorials/advanced/tutorial17/section2.htm
3. run multiple runs and repeat 1, 2
4. may be check previous publications about checking convergence.
Hai
>
> Any suggestion will be highly appreciated.
>
>
>
> thanking you,
>
> Abhsihek
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Received on Mon Oct 17 2016 - 15:00:03 PDT
