[gmx-users] FEP Calculation problem on GMX 4.5.1

[Justin A. Lemkul]

TJ Mustard wrote:
> 
> 
> On October 20, 2010 at 9:22 PM "Marcelo Brandão" 
> <brandao.marcelo at 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: mustardt at 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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