Quick question to anyone, can you extract energies and forces with g_traj and g_energy and feed them to WHAM for molecule by molecule or atom by atom PMF determination. If so, how do I get WHAM to read the extracted enrgies as they are written out. I did read something about a .pdo file if you have wierdness, that it could be used from the past?
Explanation: WHAM works fine for my system, and gives nice curves and expected values, however when I try and do this for say a particular amino acid by hand the values expected vary. I most likely am just screwing the sums (ive been using every term including rest) or theres a difference between WHAM and my means of doing the free energy change? I want to stay uniform. Any help or suggestions appriciated Sincerely Stephan Watkins -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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