Thanks for your reply. But when I don't understand why these extra lines are needed to set when are not advantageous practically! :-(
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, July 12, 2013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: > Hi, > > I want to run Umbrella Sampling on my system. In initial configurations, an > ion is located in center of the window. > Some mdp file settings for running US, as I found in US tutorial are : > ; Pull code > pull = umbrella > pull_geometry = distance > pull_dim = N N Y > pull_start = yes > pull_ngroups = 1 > pull_group0 = Chain_B > pull_group1 = Chain_A > pull_init1 = 0 > pull_rate1 = 0.0 > pull_k1 = 4000 ; kJ mol^-1 nm^-2 > pull_nstxout = 1000 ; every 2 ps > pull_nstfout = 1000 ; every 2 ps > > > But I'd like to know which lines are specifically for US? Because in this > step, no group is supposed to be pulled but there are some lines written here > related to pulling! > All of them are related to umbrella sampling. Pulling (steered MD) and umbrella sampling simply use common parts of the "pull code" in Gromacs because US requires a restraint potential. Whether or not that restraint potential induces net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate, restrain to a given set of conditions) is the only difference. Both processes require reference and "pull" groups, geometry information, etc. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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
