Re: RE: [gmx-users] Re: About entropic contribution to the potential of mean force
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 <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] Re: About entropic contribution to the >potential of mean force > To: "'Discussion list for GROMACS users'" > Message-ID: <[EMAIL PROTECTED]@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. > > ___ gmx-users mailing listgmx-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
RE: [gmx-users] Re: About entropic contribution to the potential of mean force
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 meanforce 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 listgmx-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
[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 >meanforce > 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 listgmx-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
