Dear Justin: What I mean is can I calculate the free energy of restraining the ligand in the binding site, since I put on distance restraint to the ligand and the protein?
Regards Chunxia Chunxia Gao wrote: > Dear Justin, > > If I apply the pull code to the distance restraints, can I calculate the free > energy of those restraints through g_bar? In what way? > The pull code and free energy code are independent. I see no reason why you could not proceed in the same manner as the free energy tutorial describes, but with the addition of your restraint. > and the pull code can only be applied to distance restraints, right? not > angle or dihedral restraints? > Correct. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
