Re: Equilibration "substraction" from obtained PMF from MD

From: Jerome Henin (
Date: Sat Aug 15 2009 - 16:01:01 CDT

Hi Branko,
I am just catching up now on my backlog of NAMD-l messages...

Yes, you can subtract data from the PMF. You have to do it at the
gradient level, using the ".grad" and ".count" files which give you
the gradient and number of samples in each case. If the final gradient
and number of samples are dAf and Nf, and the ones at the end of the
equilibration period are dAe and Ne, then what you want is:
dA = (Nf dAf - Ne dAe) / (Nf - Ne)

Once you have the new gradient dA, just integrate it numerically to
obtain the PMF.


On Tue, Jul 28, 2009 at 5:32 PM, Branko<> wrote:
> Hallo to all,
> I performed MD simulation of the set of small molecules in explicit solvent
> and calculated PMF by ABF of 2.7b1. Molecules are prepared by minimization
> of whole system(s) (molecule+solvent cluster), heating and MD. ABF are
> calculated only during MD, but the equilibration period is included in MD.
> Please let me know is there any way to “subtract” equilibration period from
> obtained PMF. For initial definition of ABF colvar- distances are used, as
> distance between two groups of atoms at molecule(s) “ends”. Molecules are
> flexible.
> Any advice is highly appreciated.
> Sincerely
> Branko

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