<div>Dear Angel,</div>
<div> Firstly I would quote a sentence of the manual: "Whether one needs to correct for this contribution depends on what the PMF should represent."</div>
<div> 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). </div>
<div> 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.</div>
<div> </div>
<div>zgzhang</div>
<div><br> </div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Date: Fri, 28 Nov 2008 22:55:18 +0100<br>From: ?ngel Pi?eiro <<a href="mailto:angel.pineiro@usc.es">angel.pineiro@usc.es</a>><br>
Subject: RE: [gmx-users] Re: About entropic contribution to the<br> potential of mean force<br>To: "'Discussion list for GROMACS users'" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <007401c951a4$0178f340$046ad9c0$@<a href="mailto:pineiro@usc.es">pineiro@usc.es</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Dear Zgzhang,<br><br>I am interested in your answer to your own question since I asked basically<br>
the same several months ago, could you explain it better?<br><br><br><br>Angel.<br><br></blockquote></div>