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

Ángel Piñeiro angel.pineiro at usc.es
Fri Nov 28 22:55:18 CET 2008

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?




De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
nombre de Zhang Zhigang
Enviado el: jueves, 27 de noviembre de 2008 04:28 a.m.
Para: gmx-users at gromacs.org
Asunto: [gmx-users] Re: About entropic contribution to the potential of mean


I've got it! Thanks myself. ^_^

So, it seems that the prior calculations by, i.e. Ciccotti, et al, Chem.
Phys. 129, 241 (1989), Guardia, et al, J. Chem. Phys. 95, 2823 (1991) are
flawy since they have not corrected the entropic effects at all.






Date: Wed, 26 Nov 2008 15:55:05 +0800
From: "Zhang Zhigang" <zgzhangcn at gmail.com>
Subject: [gmx-users] About entropic contribution to the potential of
       mean    force
To: gmx-users at gromacs.org
       <eb7072fb0811252355w4d9e1df9x1cc89eb3bdba3b8c at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

   In the manual of gromacs, the entropic contribution to the pmf is
emphasized. In my opinion, this contribution is originated from the
rotations of the constrained groups.
   However, according to the manual suggestion, "...when calculating a PMF
between two solutes in a solvent, for the purpose of simulating without
solvent, the entropic contribution should be removed." I'm really confused
with this.
   If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl-
and many water molecules), I want to calculate the potential of mean force
of NaCl, should I count the contributions from the entropic effects?
   According to Hess et al., (2006), JCP, 124: 164509, this effect should
surely be added.
   So, any one experienced with similar researches can give me an answer
for this: when should I add the entropic contribution to the pmfs? and, what
the really physical explanation for this effect?
   Thanks in advance!



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