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On October 20, 2010 at 9:22 PM "Marcelo Brandão" <brandao.marcelo@gmail.com> wrote:<br />
<br />
> Hello!<br />
>  I am new to this list, probably someone has have the same problem I<br />
> am facing now with the use of Gromacs to calculate FEP (Free energy<br />
> pertubaion).<br />
> I've followed the gromacs tutorial for Free energy Calculation<br />
> available at http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial,<br />
> for lambda value ranging from 0 to 1 in 11 independent job for<br />
> each lambda value.<br />
> Unfortunately, the* dVpot/dlambda  dEkin/dlambda  dG/dl constr* values<br />
> in the *.log are<br />
> continuously coming zero.<br />
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<p style="margin: 0px;">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.</p>
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> 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<br />
> for free energy calculation for Gromacs 4.5.1?<br />
><br />
> Any help will be highly appreciated.<br />
><br />
> My best regards<br />
><br />
> Marcelo Brandão<br />
><br />
><br />
> --<br />
> Marcelo Mendes Brandão<br />
> Postdoc fellow<br />
> Laboratório de Biologia Molecular de Plantas - ESALQ/USP<br />
> Website: http://bioinfo.esalq.usp.br<br />
> AtPIN: http://bioinfo.esalq.usp.br/atpin<br />
> SKYPE: mmbrand<br />
> Tel: (+55) 19 3429 4442<br />
> --<br />
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><br />
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<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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