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 >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
