Dear gromacs users I want to force the citrate to cross the channel using SMD, but when I run the tutorial Umbrella Sampling for my system adapting the entries mdp for gromacs-5.0.5 my results are staying bad!!
I want see citrato crossing the channel, and in the "generating configurations" the citrate is in left of channel and then right side of channel. How I can run this SMD protocol? I'm using the entry mdp file for pull code: ; COM PULLING pull = umbrella pull_geometry = direction pull_dim = Y N N pull_start = yes pull-print-reference = no pull_nstxout = 1000 pull_nstfout = 1000 pull_ngroups = 2 pull-ncoords = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull-group1-name = Protein ; ref pull-group2-name = CIT ; pulled pull-coord1-groups = 1 2 pull-coord1-origin = 0 0 0 pull-coord1-vec = 1 0 0 pull-coord1-init = 0 pull-coord1-rate = 0.0 pull-coord1-k = 1000 Someone can help me, please?? Bruna. Bruna Franciele Faria -Laboratory of Molecular Dynamic and Simulation UFSJ - Brazil -- 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.
