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

[Berk Hess]

Hi,

The shape of the dgdl curves also depends a lot on alpha (and sc-sigma).
>From your plots I am guessing that you are doing LJ and electrostatics
at the same time. This always results in high peaks when you have hydrogen bonding.
Things go much smoother when you first introduce the LJ interactions
and then the charges.

Berk

Date: Tue, 17 Mar 2009 23:15:52 -0300
Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again
From: fileti at ufabc.edu.br
To: gmx-users at gromacs.org

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?
Bestseef

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>

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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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