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. On Mon, Feb 25, 2013 at 3:49 PM, Ricardo O. S. Soares <rsoa...@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. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
