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. De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En nombre de Zhang Zhigang Enviado el: jueves, 27 de noviembre de 2008 04:28 a.m. Para: gmx-users@gromacs.org Asunto: [gmx-users] Re: About entropic contribution to the potential of mean force 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. Cheers, zgzhang Date: Wed, 26 Nov 2008 15:55:05 +0800 From: "Zhang Zhigang" <[EMAIL PROTECTED]> Subject: [gmx-users] About entropic contribution to the potential of mean force To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi, 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! Regards, zgzhang
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