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

Wed Mar 18 16:11:55 CET 2009

Hi,

You give too little details to understand what you do exactly.

It seems you are coupling LJ in a single simulations and Q in a single simulation
with varying lambda.
You should do this with several simulations at constant lambda values.

I think you did not specify with the plots if it was LJ or Q.
If you do LJ and Q separately, you do not need soft-core for Q.
I guess your plots were Q with soft-core. Doing Q hard-core with remove the problems.

I usually use alpha=0.6 for LJ, but slightly different values should also work fine.

You should probably read some more literature.

Berk

Date: Wed, 18 Mar 2009 11:44:13 -0300
From: fileti at ufabc.edu.br
To: gmx-users at gromacs.org
Subject: [gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)

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:

Send gmx-users mailing list submissions to

        gmx-users at gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit

        http://www.gromacs.org/mailman/listinfo/gmx-users

or, via email, send a message with subject or body 'help' to

        gmx-users-request at gromacs.org

You can reach the person managing the list at

        gmx-users-owner at gromacs.org

When replying, please edit your Subject line so it is more specific

than "Re: Contents of gmx-users digest..."

Today's Topics:

   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/

-------------- next part --------------

An HTML attachment was scrubbed...

URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090317/f3b6882b/attachment-0001.html

------------------------------

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/

_________________________________________________________________

See all the ways you can stay connected to friends and family

http://www.microsoft.com/windows/windowslive/default.aspx

-------------- next part --------------

An HTML attachment was scrubbed...

URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090318/dce60e36/attachment-0001.html

------------------------------

_______________________________________________

gmx-users mailing list

gmx-users at gromacs.org

http://www.gromacs.org/mailman/listinfo/gmx-users

Please search the archive at http://www.gromacs.org/search before posting!

End of gmx-users Digest, Vol 59, Issue 130

******************************************

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090318/cce3b9d6/attachment.html>