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 <jalem...@vt.edu
<mailto:jalem...@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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