Hi, I recommend you Justin's tutorial on Umbrella Sampling 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 > * 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
