> On 3/11/15 4:17 AM, Ming Tang wrote: > > Dear all, > > > > I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4. > > Everything was fine until I got to the step five (run the continuous pulling simulation). > > Then I turned to the 5.0.4 manual, and tried to modify the pull code, but failed. > > > > ; Pull code in tutorial > > pull = umbrella > > pull_geometry = distance ; simple distance increase > > pull_dim = N N Y > > pull_start = yes ; define initial COM distance > 0 > > pull_ngroups = 1 > > pull_group0 = Chain_B > > pull_group1 = Chain_A > > pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns > > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > > > > ; COM pulling I modified > > pull = umbrella > > pull_geometry = distance ; simple distance increase > > pull_dim = N N Y > > pull_start = yes ; define initial COM distance > 0 > > pull_coord1-groups = 2
Group 1 & 2 participating in reaction coordinate So it is wrong to state just group 2 in pull_coord1-groups = 2 change it to : pull_coord1_groups = 1 2 > > pull-group1-name = Chain_B > > pull_group2-name = Chain_A > > pull-coord1-rate = 0.01 ; 0.01 nm per ps = 10 nm per ns > > pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 > > > > Fatal error: > > Group Chain_B referenced in the .mdp file was not found in the index file. > > Group names must match either [moleculetype] names or custom index group > > names, in which case you must supply an index file to the '-n' option > > of grompp. > > > > Could anybody tell me what's wrong with the COM pulling code I modified? > > Best Regards, Nima Soltani ---------------------------------------------------------- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology. ================================= -- 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.