<div class="gmail_quote">
<div>I've got it! Thanks myself. ^_^</div>
<div>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.</div>
<div> </div>
<div>Cheers,</div>
<div> </div>
<div>zgzhang</div>
<div> </div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span>Date: Wed, 26 Nov 2008 15:55:05 +0800<br>From: "Zhang Zhigang" <<a href="mailto:zgzhangcn@gmail.com">zgzhangcn@gmail.com</a>><br>
Subject: [gmx-users] About entropic contribution to the potential of<br> mean force<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <<a href="mailto:eb7072fb0811252355w4d9e1df9x1cc89eb3bdba3b8c@mail.gmail.com">eb7072fb0811252355w4d9e1df9x1cc89eb3bdba3b8c@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br> In the manual of gromacs, the entropic contribution to the pmf is<br>emphasized. In my opinion, this contribution is originated from the<br>rotations of the constrained groups.<br>
However, according to the manual suggestion, "...when calculating a PMF<br>between two solutes in a solvent, for the purpose of simulating without<br>solvent, the entropic contribution should be removed." I'm really confused<br>
with this.<br> If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl-<br>and many water molecules), I want to calculate the potential of mean force<br>of NaCl, should I count the contributions from the entropic effects?<br>
According to Hess et al., (2006), JCP, 124: 164509, this effect should<br>surely be added.<br> So, any one experienced with similar researches can give me an answer<br>for this: when should I add the entropic contribution to the pmfs? and, what<br>
the really physical explanation for this effect?<br> Thanks in advance!<br><br>Regards,<br><br>zgzhang<br></blockquote></div>