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Hi,<br><br>You give too little details to understand what you do exactly.<br><br>It seems you are coupling LJ in a single simulations and Q in a single simulation<br>with varying lambda.<br>You should do this with several simulations at constant lambda values.<br><br>I think you did not specify with the plots if it was LJ or Q.<br>If you do LJ and Q separately, you do not need soft-core for Q.<br>I guess your plots were Q with soft-core. Doing Q hard-core with remove the problems.<br><br>I usually use alpha=0.6 for LJ, but slightly different values should also work fine.<br><br>You should probably read some more literature.<br><br>Berk<br><br><hr id="stopSpelling">Date: Wed, 18 Mar 2009 11:44:13 -0300<br>From: fileti@ufabc.edu.br<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)<br><br><div>Berk Hello, thank you for your attention. </div><div>My system has 24 hydroxyl groups, and in ethanol, there should be more than 20 solute-solvent hydrogen bonds </div><div>being erased simultaneously (not to mention the possible intramolecular HB's).</div>
<div><br></div><div>I did the simulation using the following protocol:</div><div><br></div><div>1) I made disappear the electrostatic interactions turning off the charges (by 200ps), </div><div>2) At the sequence I made disappear the LJ interactions (for more 200ps) </div>
<div>3) Finally I performed a run of 0.5ns.</div><div><br></div><div>Do you think I should extend further the time of the simulations? </div><div>This will solve the huge peak at lambda = 0? </div><div><br></div><div>One more thing. Sorry, but so far I can not understood the reason </div>
<div>for not to use sc-power=2, which in this case can reduce dramatically </div><div>the errors associated with the integral of dG/dlambda.</div>_______________________________________<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><br><div class="EC_gmail_quote">On Wed, Mar 18, 2009 at 8:00 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="EC_gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. RE: Softcores: sc-power = 1 or 2 ? again (Eudes Fileti)<br>
2. RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 17 Mar 2009 23:15:52 -0300<br>
From: Eudes Fileti <<a href="mailto:fileti@ufabc.edu.br">fileti@ufabc.edu.br</a>><br>
Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:65e289a20903171915jd34087epa77c0d0908af9103@mail.gmail.com">65e289a20903171915jd34087epa77c0d0908af9103@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello Berk, I have tried to calculate the free energy of transfer<br>
for a polyhydroxylated (from benzene to ethanol).<br>
The Dg/dlambda plot, for both, benzene and ethanol shows a<br>
very high and narrow peak near lambda=0. In the case of ethanol<br>
is worse due to the solute-solvent hydrogen bonds.<br>
<br>
I performed two sets of simulations, one for sc-power=1 and another<br>
for sc-power=2. For sc-power=1 I got a peak much higher than for<br>
sc-power=2, and therefore the integration in this case (sc-power=1)<br>
could lead me to a much greater error. (please see figure<br>
<a href="http://cromo.ufabc.edu.br/%7Efileti/web/dgdl-transfer2.jpg">http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg</a>)<br>
In both cases (ethanol and benzene) the curves coincide for values of lambda<br>
beyond 0.4.<br>
<br>
That is the why of my original question. Not in this case is justified<br>
use sc-power=2? Have you any tips on how to ensure the accuracy of<br>
calculation of Delta_G in this case?<br>
<br>
Bests<br>
eef<br>
<br>
<br>
Message: 3<br>
Date: Tue, 17 Mar 2009 15:49:12 +0100<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] Softcores: sc-power = 1 ou 2 ?<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-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">fileti@ufabc.edu.br</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Softcores: sc-power = 1 ou 2 ?<br>
<br>
Hello, I have a doubt regarding the use of soft-core. When the use of<br>
sc-power = 2 is more recommended than sc-power =<br>
1?eef_______________________________________<br>
Eudes Eterno Fileti<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/">http://cromo.ufabc.edu.br/~fileti/</a><br>
_______________________________________<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>
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Message: 2<br>
Date: Wed, 18 Mar 2009 11:07:02 +0100<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <COL113-W565A4B17F474C3559010A08E990@phx.gbl><br>
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<br>
<br>
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>
Date: Tue, 17 Mar 2009 23:15:52 -0300<br>
Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again<br>
From: <a href="mailto:fileti@ufabc.edu.br">fileti@ufabc.edu.br</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
Hello Berk, I have tried to calculate the free energy of transfer for a polyhydroxylated (from benzene to ethanol). The Dg/dlambda plot, for both, benzene and ethanol shows a<br>
very high and narrow peak near lambda=0. In the case of ethanol is worse due to the solute-solvent hydrogen bonds.<br>
I performed two sets of simulations, one for sc-power=1 and another<br>
for sc-power=2. For sc-power=1 I got a peak much higher than for sc-power=2, and therefore the integration in this case (sc-power=1) 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>)<br>
In both cases (ethanol and benzene) the curves coincide for values of lambda beyond 0.4.<br>
That is the why of my original question. Not in this case is justified use sc-power=2? Have you any tips on how to ensure the accuracy of<br>
calculation of Delta_G in this case?<br>
Bestseef<br>
<br>
Message: 3<br>
Date: Tue, 17 Mar 2009 15:49:12 +0100<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
<br>
Subject: RE: [gmx-users] Softcores: sc-power = 1 ou 2 ?<br>
<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<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>
<br>
From: <a href="mailto:fileti@ufabc.edu.br">fileti@ufabc.edu.br</a><br>
<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
Subject: [gmx-users] Softcores: sc-power = 1 ou 2 ?<br>
<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 Fileti<br>
<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/">http://cromo.ufabc.edu.br/~fileti/</a><br>
_______________________________________<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>
<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>
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