[gmx-users] Re: Free energy with Gromacs.

[Justin A. Lemkul]

Again, *please keep all Gromacs-related correspondence on the mailing list*  The 
type of information that you have posted is important to share with others who 
may know how to help.  I do not know the answer to your problem.  I would 
suggest contacting the list again with the following information:

1. The relevant contents of your .mdp file(s)
2. What each figure in your image represents (main image vs. inset)

-Justin

Eudes Fileti wrote:
> Justin thanks for the reply. 
> Sorry, 160000 refers to the value of dg / dl for lambda = 0. 
> I am sending you a link for you see the profile of the curve.
> http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg
> This case is for solute in benzene. The peak in lambda=0 is around 30000.
> 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. 
> In both cases (ethanol and benzene) the curves coincide for values of 
> lambda beyond 0.4.
> bests
> eef
> 
> P.S.: I am using the 3.3.3 version.
> 
> _______________________________________
> 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 7:13 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Eudes Fileti wrote:
> 
>         Hello Justin, I am facing a very similar problem to that you
>         experienced and described in
>         (http://www.gromacs.org/pipermail/gmx-users/2008-February/032429.html).
> 
>         I throw this question in the GMX forum and Berk has kindly
>         helped me. But reading the forum I realized that you already
>         could be solved the problem so that maybe I could help more
>         directly.
> 
> 
>     Please keep Gromacs-related discussions on the list.  If you had
>     followed the rest of the thread you reference, you will find that my
>     calculations were falling victim to a bug in Gromacs-3.3.1.  If you
>     are using a newer version, then my situation is not applicable,
>     since the problem has been fixed (IIRC) as of Gromacs-3.3.3.
> 
>     If you are using version 3.3.1, re-run your simulations with a newer
>     version.
> 
> 
>         I have tried to calculate the free energy of transfer from
>         benzene to ethanol
>         for a polyhydroxylated (24 OH's). This 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).
> 
>         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, 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.
>         Correct me i this procedure is inappropriate.
> 
>         To start, Berk said me that the use of sc-power=2 never is
>         recommended. Ok!
>         Secondly, then he gave me a good tip that I was not taking into
>         account:
>         Disappear the electrostatic interactions using hard-core instead
>         soft-core.
>         I did this and actually work (only in part).
> 
>         When I used softcore to desappear the electrostatic interations,
>         the value of dg/dlambda for lambda = 0 was ~160000. Following
>         the tip of Berk, wiht hardcore I got ~2000!
> 
> 
>     Right, you should only need soft-core for the LJ component.
> 
> 
>         However when I needed to use softcore again, now to remove the
>         LJ interactions, the value returned back to ~160000.`
> 
> 
>     I don't understand what you mean.  Is the total area under the curve
>     160000? That is ridiculously high.
> 
>     I don't know that I have the expertise to help you much more.  I am
>     not entirely familiar with your methodology.  What I have done in my
>     own work is run 21 independent simulations at lambda points between
>     0 and 1 (5 ns each after equilibration), and integrated the
>     resulting curve.  None of my dV/dl points ever approached that
>     magnitude, but I can't comment on your specific case, because I
>     don't know what you're doing.
> 
>     -Justin
> 
> 
>         Could you gimme some insigths to solve this problem?
>         Best
>         eef
> 
>         P.S.: You can solve your problem of polyphenolic compound?
> 
>         _______________________________________
>         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/
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================