Allright. As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system. An ion is considered in center of the each window, the reaction coordinate is set to z, so the group which is pulled is an ion, and my ref group would be COM of the protein. But I don't know what statement is supposed to write in mdp settings exactly: ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = COM of protein pull_group1 = ion 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
IN fact, to implement such settings, how I make the US understand to get the COM of protein as the ref group and the proposed ion as the pulled group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 5:10 PM, Shima Arasteh wrote: > Thanks for your reply. > > But when I don't understand why these extra lines are needed to set when are > not advantageous practically! :-( > There's nothing "extra." Everything here has a functional purpose. -Justin > > 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 -- 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
