Hi everybody, I would like to pull a ligand in a channel from my protein and calculate the PMF with Umbrella sampling. This channel is probably not linear and thus have to be defined. Too much colisions appears along a simple one axis pulling and causing a catastrophic PMF calculation.
Currently I'm working with Gromacs and I wondered if it is possible to define statically or dynamically the coordinates for the center of the channel and use it during the simulation (Pulling). One solution could be to define in the md_pull.mdp configuration file all the transition points of my pathway through which my ligand must pass from my APO structure determined with CAVER. Instantiation of Gromacs parameters of md_pull.mdp is not enough clear for me and PLUMED is may be a more direct solution. Currently I have no experience with PLUMED but It seems on paper to be able. An other choice would be to define dynamically the channel center, on-the-fly. PLUMED seems also capable to manage this sort of challenge but once again I have no idea of the feasibility of a such work. What do you think about this problem and of the tracks evoked above ? Cheers, FR. *Pulling inside a channel to calculate the PMF*. Available from: https://www.researchgate.net/post/Pulling_inside_a_channel_to_calculate_the_PMF#594b792648954cf7f2759a48 [accessed Jun 22, 2017]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.