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 > <[email protected]> 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 [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. * Can't post? > Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
