[gmx-users] How to perform RAMD in gromacs -reg
Dear Gromacs users/developers, To study ligand disassociation from binding pocket of protein, how do implement in RAMD in gromacs searched for tutorial, am not getting any relevant, could you don't mind can share that info/procedure proceed further. Thank you Sincerely s.venkatesh -- 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.
Re: [gmx-users] Gmx mindist
Also i have used this command G_mindist -f md2.gro -s -n -or (select Pr-H and tube) Dies it calculate minimum distabce of non-hydrogen atom of each residue with tube closest atom or COM of nanotube? On Mon, 31 Dec 2018, 03:03 rose rahmani Hi, > > Does g_mindist calculates distances between COM of two groups? > > I want twi calculate dustances between any atom of protein-H and nanotube > surface. So if g_mindist shows for example 0.9nm is it really 0.9-0.7(tube > radius)=0.2 nm from surface? > > Best > -- 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.
[gmx-users] Gmx mindist
Hi, Does g_mindist calculates distances between COM of two groups? I want twi calculate dustances between any atom of protein-H and nanotube surface. So if g_mindist shows for example 0.9nm is it really 0.9-0.7(tube radius)=0.2 nm from surface? Best -- 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.
