[gmx-users] Re: About entropic contribution to the potential of mean force

[Zhang Zhigang]

Dear Angel,
    Firstly I would quote a sentence of the manual: "Whether one needs to
correct for this contribution depends on what the PMF should represent."
   Secondly, in my opinion, the so-called entropic contribution to the PMF
(we abbreviate it as P0) is a kind of reference PMF. That is to say, P0 is
just the PMF of two non-interacting masses (originated from centrifugal
force).
   So, if we are interested in the "absolute" PMF, e.g. pull a substrate
into a protein, P0 is surely not be substracted from PMF; otherwise, if we
are interested in "excess" PMF, e.g. ionic PMF with the aim of inversion of
radial distribution function (which is calculated with the reference of
ideal gas), then P0 should be removed.

zgzhang



> Date: Fri, 28 Nov 2008 22:55:18 +0100
> From: ?ngel Pi?eiro <angel.pineiro at usc.es>
> Subject: RE: [gmx-users] Re: About entropic contribution to the
>        potential       of      mean force
> To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
> Message-ID: <007401c951a4$0178f340$046ad9c0$@pineiro at usc.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Zgzhang,
>
> I am interested in your answer to your own question since I asked basically
> the same several months ago, could you explain it better?
>
>
>
> Angel.
>
>
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