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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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