[gmx-users] Softcores: sc-power = 1 or 2 ? again

[Eudes Fileti]

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
very high and narrow peak near lambda=0. In the case of ethanol
is worse due to the solute-solvent hydrogen bonds.

I performed two sets of simulations, one for sc-power=1 and another
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
http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg)
In both cases (ethanol and benzene) the curves coincide for values of lambda
beyond 0.4.

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
calculation of Delta_G in this case?

Bests
eef


Message: 3
Date: Tue, 17 Mar 2009 15:49:12 +0100
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] Softcores: sc-power = 1 ou 2 ?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <COL113-W468577C913D7E1AF9301238E980 at phx.gbl>
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Hi,

Never (unless you want to reproduce old simulations).

Berk

Date: Tue, 17 Mar 2009 10:50:48 -0300
From: fileti at ufabc.edu.br
To: gmx-users at gromacs.org
Subject: [gmx-users] Softcores: sc-power = 1 ou 2 ?

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_______________________________________
Eudes Eterno Fileti

Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
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