[gmx-users] Re: Free energy with Gromacs.
David Mobley
dmobley at gmail.com
Fri Apr 10 15:49:19 CEST 2009
You may also want to look at www.alchemistry.org, as it has some
general information about how these should be set up.
On Wed, Mar 18, 2009 at 8:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> 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
>
> ========================================
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