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Hi,<br><br>The shape of the dgdl curves also depends a lot on alpha (and sc-sigma).<br>From your plots I am guessing that you are doing LJ and electrostatics<br>at the same time. This always results in high peaks when you have hydrogen bonding.<br>Things go much smoother when you first introduce the LJ interactions<br>and then the charges.<br><br>Berk<br><br><hr id="stopSpelling">Date: Tue, 17 Mar 2009 23:15:52 -0300<br>Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again<br>From: fileti@ufabc.edu.br<br>To: gmx-users@gromacs.org<br><br><span class="EC_Apple-style-span" style="border-collapse: collapse;"><div><div>Hello Berk, I have tried to calculate the free energy of transfer </div><div>for a polyhydroxylated (from benzene to ethanol). </div><div>The Dg/dlambda plot, for both, benzene and ethanol shows a </div>
<div>very high and narrow peak near lambda=0. In the case of ethanol </div><div>is worse due to the solute-solvent hydrogen bonds. </div><div><br></div><div>I performed two sets of simulations, one for sc-power=1 and another </div>
<div>for sc-power=2. For sc-power=1 I got a peak much higher than for </div><div>sc-power=2, and therefore the integration in this case (sc-power=1) </div><div>could lead me to a much greater error. (please see figure <a href="http://cromo.ufabc.edu.br/%7Efileti/web/dgdl-transfer2.jpg">http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg</a>) </div>
<div>In both cases (ethanol and benzene) the curves coincide for values of lambda beyond 0.4. </div><div><br></div><div>That is the why of my original question. Not in this case is justified </div><div>use sc-power=2? Have you any tips on how to ensure the accuracy of </div>
<div>calculation of Delta_G in this case?</div><div><br></div><div>Bests</div><div>eef</div></div><div><br></div><div><br></div>Message: 3<br>Date: Tue, 17 Mar 2009 15:49:12 +0100<br>From: Berk Hess <<a href="mailto:gmx3@hotmail.com" style="color: rgb(0, 0, 204);">gmx3@hotmail.com</a>><br>
Subject: RE: [<span class="EC_il" style="background-color: rgb(255, 255, 136);">gmx</span>-users] Softcores: sc-power = 1 ou 2 ?<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" style="color: rgb(0, 0, 204);"><span class="EC_il" style="background-color: rgb(255, 255, 136);">gmx</span>-users@gromacs.org</a>><br>
Message-ID: <COL113-W468577C913D7E1AF9301238E980@phx.gbl><br>Content-Type: text/plain; charset="iso-8859-1"<br><br><br>Hi,<br><br>Never (unless you want to reproduce old simulations).<br><br>Berk<br><br>Date: Tue, 17 Mar 2009 10:50:48 -0300<br>
From: <a href="mailto:fileti@ufabc.edu.br" style="color: rgb(0, 0, 204);"><span class="EC_il" style="background-color: rgb(255, 255, 136);">fileti</span>@ufabc.edu.br</a><br>
To: <a href="mailto:gmx-users@gromacs.org" style="color: rgb(0, 0, 204);"><span class="EC_il" style="background-color: rgb(255, 255, 136);">gmx</span>-users@gromacs.org</a><br>
Subject: [<span class="EC_il" style="background-color: rgb(255, 255, 136);">gmx</span>-users] Softcores: sc-power = 1 ou 2 ?<br>
<br>Hello, I have a doubt regarding the use of soft-core. When the use of sc-power = 2 is more recommended than sc-power = 1?eef_______________________________________<br>Eudes Eterno <span class="EC_il" style="background-color: rgb(255, 255, 136);">Fileti</span><br>
<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>09210-170 Santo André - SP Brasil<br>+55.11.4437-8408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/%7Efileti/" style="color: rgb(0, 0, 204);">http://cromo.ufabc.edu.br/~<span class="EC_il" style="background-color: rgb(255, 255, 136);">fileti</span>/</a></span><br clear="all">
_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>09210-170 Santo André - SP Brasil<br>
+55.11.4437-8408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/%7Efileti/">http://cromo.ufabc.edu.br/~fileti/</a><br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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