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
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Received on Mon Nov 18 2013 - 14:00:02 PST
