[gmx-users] problem calculating PMF with distant constraints

Berk Hess gmx3 at hotmail.com
Fri Dec 16 11:54:04 CET 2005

>From: rzangi at att.net
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] problem calculating PMF with distant constraints
>Date: Thu, 15 Dec 2005 23:25:14 +0000
> > >>
> > >>>I am trying to calculate potential of mean force between two atoms 
> > >>
> > >>methane) by running multiples simulations with distances that are 
> > >>from lambda=0 to lambda=1 and then integrating <dHdl>. However, this 
> > >>seem to give the right curve as compare to calculations obtained with 
> > >>methods. There appears to be a serious discrepancy.
> > >>
> > >>the dHdl curve is meaningless, only the integral is physcially
> > >>meaningfull. Of course you can compare to other simulations done in an
> > >>identical fashion.
> > >
> > >
> > > We compared difference free energies (i.e. the PMF curves 
>supperimposed on
> > each other) with identical settings and interaction parameters.
> > >
> > There are many hidden parameters, not only in gromacs but also in other
> > programs, like combination rules.
> > By the way you still don't say how you compute it.
>We used the same combination rule as the reference and also used the second 
>type of combination rule.
>Below is one of the topology files. Similar results we got also with SPC, 
>SPCE and tip5p, and also with different LJ particles.
>The locations of the minimums of the PMF are good but the depth at contact 
>is higher than the state at large distances, where is should be lower.

This sounds like you might have forgotten about the trivial volume or 
entropy term.
You can not directly integrate the constraint force.
You need to correct for the fact that the volume sampled by the two 
increases with the constraint length.
The free-energy volume contribution is:
-2 k T log(r)
The force thus is:
2 k T / r


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