[gmx-users] free energy question
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 21 09:10:02 CET 2003
On Fri, 2003-11-21 at 00:09, Yuhua Song wrote:
> 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,
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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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