Of course I read Justin's tutorial. The reason I am asking is that I am not sure how to do it.
On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani < [email protected]> 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 > > Regards > > Arman > > On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov <[email protected]> > 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 [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Netaly -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
