[gmx-users] free energy question

[David van der Spoel]

On Fri, 2003-11-21 at 15:41, Yuhua Song wrote:
> Thanks David for your kind response. my questions: for the calculation of
> free energy, the dg/dl came from the whole system energy or from the protein
> energy?
by definition it is for the whole system.

> 
> Thanks,
> 
> Yuhua
> 
> ----- Original Message ----- 
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: <gmx-users at gromacs.org>
> Sent: Friday, November 21, 2003 2:07 AM
> Subject: Re: [gmx-users] free energy question
> 
> 
> > On Fri, 2003-11-21 at 00:09, Yuhua Song wrote:
> > > Hi,
> > >
> > > I have a system with protein, water and ions and with one ion binded at
> the
> > > binding site of protein. I intend to replace the binded metal ion with
> > > another metal ion to calculate the free energy change. After the whole
> > > system equilibration, I do the free energy perturbation following the
> manual
> > > of Gromacs to do the free energy perturbation using the thermodynamics
> > > method. My questions is: in preparing the *.mdp file, in the section of
> > > energy monitoring: energygrps: I should output the whole system energy,
> or
> > > protein, ions, water energy separately? which is the best way for me to
> > > caculate the free energy perturbation caused by replacing the metal ion
> at
> > > the binding site of protein?
> > >
> > > Also, how to calculate the free energy with the g_cluster way? such as:
> for
> > > the whole system, some part the protein conformation change is not big,
> but
> > > some part of the protein conformation change is big. In this situation,
> > > which is the best way for me to calculate the free energy perturbation?
> > > g_cluster? then how to use g_cluster to realize it?
> > >
> > if you run free energy, the relevant variable will end up in the energy
> > file, or optionally in a file dgdl.xvg
> >
> >
> > > Thank you very much in advance,
> > >
> > > Yuhua
> > >
> > >
> > > _______________________________________________
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> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
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> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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