[gmx-users] free energy question
yhsong at ccb.wustl.edu
Fri Nov 21 15:43:00 CET 2003
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
----- 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
> > 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
> > 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,
> > protein, ions, water energy separately? which is the best way for me to
> > caculate the free energy perturbation caused by replacing the metal ion
> > the binding site of protein?
> > Also, how to calculate the free energy with the g_cluster way? such as:
> > the whole system, some part the protein conformation change is not big,
> > 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 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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