Dear All, I've performed TMD simulation using NAMDprogram. I'd like to calculate PMF plot based on the frames that were taken from TMD simulations by using GROMACS. The coordinate of reaction is RMSD of backbone. The first step is to do Umbrella sampling. The question is how fix the position of backbone during the Umbrella sampling? Is this looks reasonable?
pull = umbrella pull_geometry = position ;pull_dim = Y Y Y pull_start = yes pull_ngroups = 1 ;pull_group0 =0 pull_group1 = backbone pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps Any ideas how to convert the reaction coordinate from position of backbone to RMSD of backbone in PMF plot? Thank you in advance. Netaly Khazanov -- Netaly -- 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
