Yes, I got Thomas response and I am so grateful in this about. :-) Also many many thanks for your response Justin.
Although I don't know the definition of pull-vec yet and I need to study in this about, Would you please let me know if the grompp knows what I wrote as the COM of protein or not? And if it recognizes which ion I mean to be pulled among many ions exist in the whole system? How is it? 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 8:16 PM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/12/13 11:32 AM, Shima Arasteh wrote: > > > > 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? > You got a very thorough response already today: http://lists.gromacs.org/pipermail/gmx-users/2013-July/082855.html I see that your settings are now different, using "position" geometry instead of "distance," which is good because that's a better approach for your system. What you haven't specified is pull_vec1, which is necessary when using "position" geometry. All of these details are discussed to some extent in my umbrella sampling tutorial; it should certainly serve as a basic guide. What you're trying to do is ultimately going to require a slightly different approach, but the general principles and explanations of .mdp terms are the same. -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
