Thanks. However, I can restrain the position of backbone (x,y,z -coordinates) while running umbrella sampling and treat it like reaction coordinate. Is it right?
Maybe I am missing something. pull = umbrella pull_geometry = position ;pull_dim = Y Y Y pull_start = yes pull_ngroups = 1 ;pull_group0 =0 pull_group1 = backbone pull_init1 = 0 pull_rate1 = 0.0 On Wed, Oct 17, 2012 at 2:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/17/12 5:44 AM, Netaly Khazanov wrote: > >> Of course I read Justin's tutorial. >> The reason I am asking is that I am not sure how to do it. >> >> > As far as I am aware, there is no way to conduct umbrella sampling in this > way using Gromacs. The PMF calculations that Gromacs does are based on > restrained distances or angles. I do not believe one can set an arbitrary > variable like RMSD to be a reaction coordinate in the same sense, and > certainly the pull code is not applicable in this instance. > > -Justin > > > On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani < >> armansoufi...@gmail.com> wrote: >> >> Hi, >>> >>> I recommend you Justin's tutorial on Umbrella Sampling >>> >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >>> gmx-tutorials/umbrella/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html> >>> >>> Regards >>> >>> Arman >>> >>> On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov <neta...@gmail.com> >>> wrote: >>> >>> Dear All, >>>> >>>> I've performed TMD simulation using NAMDprogram. I'd like to calculate >>>> >>> PMF >>> >>>> plot based on the frames that were taken from TMD simulations by using >>>> GROMACS. >>>> The coordinate of reaction is RMSD of backbone. >>>> The first step is to do Umbrella sampling. The question is how fix the >>>> position of backbone during the Umbrella sampling? >>>> Is this looks reasonable? >>>> >>>> pull = umbrella >>>> pull_geometry = position >>>> ;pull_dim = Y Y Y >>>> pull_start = yes >>>> pull_ngroups = 1 >>>> ;pull_group0 =0 >>>> pull_group1 = backbone >>>> pull_init1 = 0 >>>> pull_rate1 = 0.0 >>>> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >>>> pull_nstxout = 1000 ; every 2 ps >>>> pull_nstfout = 1000 ; every 2 ps >>>> >>>> Any ideas how to convert the reaction coordinate from position of >>>> >>> backbone >>> >>>> to RMSD of backbone in PMF plot? >>>> >>>> Thank you in advance. >>>> >>>> Netaly Khazanov >>>> -- >>>> Netaly >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> * Please search the archive at >>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>>> >>>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >> >> >> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Netaly -- 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
