TJ Mustard wrote:
On October 20, 2010 at 9:22 PM "Marcelo Brandão"
<brandao.marc...@gmail.com> wrote:
> Hello!
> I am new to this list, probably someone has have the same problem I
> am facing now with the use of Gromacs to calculate FEP (Free energy
> pertubaion).
> I've followed the gromacs tutorial for Free energy Calculation
> available at
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial,
> for lambda value ranging from 0 to 1 in 11 independent job for
> each lambda value.
> Unfortunately, the* dVpot/dlambda dEkin/dlambda dG/dl constr* values
> in the *.log are
> continuously coming zero.
I did this but with gaff and amber03 ff and it worked out fine. I have
no idea why you are getting dVpot/dLambda= 0. I would make sure you have
all the settings set correctly.
Posting an .mdp file would greatly improve the odds of getting this figured out.
If you're getting all zeros, you probably aren't actually interpolating
between the A and B states. Note that the free energy code underwent a major
overhaul between version 3.3.3 and 4.0, so the tutorial linked above may not be
entirely applicable any more. It is certainly useful in a general sense, but
many of the .mdp settings have changed.
-Justin
> I Can use g_analyse, g_lie and g_energy but all results in zero.>
Does anyone has any idea on what is going on? Is there any tutorial
> for free energy calculation for Gromacs 4.5.1?
>
> Any help will be highly appreciated.
>
> My best regards
>
> Marcelo Brandão
>
>
> --
> Marcelo Mendes Brandão
> Postdoc fellow
> Laboratório de Biologia Molecular de Plantas - ESALQ/USP
> Website: http://bioinfo.esalq.usp.br
> AtPIN: http://bioinfo.esalq.usp.br/atpin
> SKYPE: mmbrand
> Tel: (+55) 19 3429 4442
> --
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>
TJ Mustard
Email: musta...@onid.orst.edu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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