Dear Colleagues,
I am trying to do an umbrella sampling using a series of conformations extracted from several unbiased MD trajectories. But I am not sure about the pull code in .mdp file. Below is the pull code from the tutorial of Dr. Justin Lemkul : define = -DPOSRES_B ; (Why ??) ; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = Chain_B pull_group2_name = Chain_A pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate = 0.0 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Conformations in Justin's tutorial are from steered MD. However, my conformations are not from SMD, and I have not done SMD on this system. So, how to define pull_group1 and pull_group2? And pull_coord1_geometry still set to "distance" ? Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? Why? Any one can provide a template of pull code for such simulations? Thanks a lot Qing Lv -- 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.
