[gmx-users] problem calculating PMF with distant constraints
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 16 13:25:44 CET 2005
Berk Hess wrote:
>> 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 (neon,
>> > >>
>> > >>methane) by running multiples simulations with distances that are
>> > >>from lambda=0 to lambda=1 and then integrating <dHdl>. However,
>> this doesn't
>> > >>seem to give the right curve as compare to calculations obtained
>> with other
>> > >>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
Does this apply to any PMF calculation, even when no constraints are
involved (i.e. measuring the force at discrete distances)?
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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