[gmx-users] g_bar for larger systems (protein-protein interaction)

[Ricardo Soares]

On Mon, 25 Feb 2013 15:55:05 -0500, Michael Shirts wrote
> My personal opinion is that for large protein-protein calculations,
> the free energy should be computed through potential of mean force
> calculations, NOT alchemical methods, using the endpoints (properly
> corrected) to determine the free energy of association.
> 
> There are a number of tutorials and example papers on how to compute
> these potentials of mean force, so I won't go into those details here.


I see Michaels, thanks for your reply!


> 
> On Mon, Feb 25, 2013 at 3:49 PM, Ricardo O. S. Soares
> <rsoares at fcfrp.usp.br> wrote:
> > Hello dear users,
> >
> > I just took a look at the new gromacs paper at Bioinformatics, and I noticed
> > a new tool g_bar, which is used for free energy calculations. I also found a
> > nice tutorial by Justin Lemkul. While I'm adapting the workflow to my
> > system, I'd like to know from anyone with more expertise in this field, if
> > this method can be successfully applied to larger molecules as ligands,
> > other than small organic ligands. What is the effectiveness in determining a
> > protein-protein (300+ residues) energy of binding, if any?
> >
> > Thanks,
> >
> > Ricardo.
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