thank you so much @Quyen Vu. I'll get back to you soon. On Mon, Apr 8, 2019 at 7:00 PM Quyen Vu <vuqv.p...@gmail.com> wrote:
> Hi Naveen, > I think you are looking for absolute reference position in space, which is > mention on page 436 of manual 2019.1 > In my case, I pull ACE residue. > my pulling code is: > pull = yes > pull_ncoords = 1 ; only one reaction coordinate > pull_ngroups = 1 ; two groups defining one reaction > coordinate > pull_coord1_groups = 0 1 > pull_group1_name = ACE > pull_coord1_type = umbrella ; harmonic potential > pull_coord1_geometry = direction ; simple distance increase > pull-coord1-vec = 1.0 0.0 0.0 > pull_coord1_dim = Y N N > pull_coord1_start = yes ; define initial COM distance > 0 > pull-coord1-origin = 18.0 5.19 5.06 ; absoulte reference point > pull_coord1_rate = 0.005 ; 0.005 nm per ps = 5 nm per ns > pull_coord1_k = 600 ; kJ mol^-1 nm^-2 > > ;********************************************************************************* > Hope my code is useful with you or if I wrong, someone can correct me. > Best regards, > Quyen > > On Mon, Apr 8, 2019 at 8:20 AM Naveen BK <naveenbk4...@gmail.com> wrote: > > > Dear all, > > > > This question is regarding Umbrella sampling. My group 1 is substrate and > > group 2 protein. Trying to pull the substrate molecule from the active > site > > pocket. In all the cases(for group 2), I used either atom or residue for > > the center of mass [COM]. Now I want to run a simulation by considering > > that COM of protein which may be present in the vacuum or in the empty > > space. In other words, I don't want to fix any atom or residue of the > > protein but I want to fix an empty space. I was not able to find any > > solutions regarding this if anyone could help me to figure it, would be > > great. > > > > -- > > Thanks and Regards, > > Naveen Krishna > > +91 8123474717 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Regards, Naveen Krishna 8123474717 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
