[gmx-users] correction of pmf profile due to entropic decrease

[Erik Marklund]

Dear Alex,

No. First of all, this is taken care of by gmx wham if I remember correctly. And it does so by looking at the dimensionality of your umbrella sampling setup. Secondly, there are cases where you don’t want that correction at all. The manual mentions one such example. In such cases the entropic contribution must be removed.

Kind regards,
Erik

> On 7 Dec 2016, at 19:33, Alex <alexanderwien2k at gmail.com> wrote:
> 
> Any suggestion please?
> Thank you.
> 
> 
> On Tue, Dec 6, 2016 at 1:16 PM, Alex <alexanderwien2k at gmail.com> wrote:
> 
>> 
>> Hello gmx user,
>> 
>> Do we need always correct the PMF profile from US by the
>> "$k_{B}T*log[4π(\epsilon)^2]$" factor in which epsilon is reaction
>> coordinate in order to removes the entropic decrease? as been mentioned
>> here:
>> 
>> 10.1021/ct100494z
>> 
>> Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory
>> Comput.2010,6, 3713-3720
>> 
>> Best regards,
>> Alex
>> 
>> 
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