[gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)

Wed Mar 18 15:44:13 CET 2009

Berk Hello, thank you for your attention.
My system has 24 hydroxyl groups, and in ethanol, there should be more than
20 solute-solvent hydrogen bonds
being erased simultaneously (not to mention the possible intramolecular
HB's).

I did the simulation using the following protocol:

1) I made disappear the electrostatic interactions turning off the charges
(by 200ps),
2) At the sequence I made disappear the LJ interactions (for more 200ps)
3) Finally I performed a run of 0.5ns.

Do you think I should extend further the time of the simulations?
This will solve the huge peak at lambda = 0?

One more thing. Sorry, but so far I can not understood the reason
for not to use sc-power=2, which in this case can reduce dramatically
the errors associated with the integral of dG/dlambda.
_______________________________________
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/

On Wed, Mar 18, 2009 at 8:00 AM, <gmx-users-request at gromacs.org> wrote:

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>   1. RE: Softcores: sc-power = 1 or 2 ? again (Eudes Fileti)
>   2. RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 17 Mar 2009 23:15:52 -0300
> From: Eudes Fileti <fileti at ufabc.edu.br>
> Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again
> To: gmx-users at gromacs.org
> Message-ID:
>        <65e289a20903171915jd34087epa77c0d0908af9103 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> 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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> Message: 2
> Date: Wed, 18 Mar 2009 11:07:02 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W565A4B17F474C3559010A08E990 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> 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>
>
> Message-ID: <COL113-W468577C913D7E1AF9301238E980 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> 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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