Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds in pure md is not directional, as it should be.
can molecular dynamics (md) simulate heavy metals, like iron, which have d oribtals? I heard that even calcium is a bit troublesome in md. On Wed, Oct 15, 2014 at 1:22 PM, Guangyu Zhu <g...@hwi.buffalo.edu> wrote: > Hi, I’m a beginner of gromacs. I want to do simulation for a protein with > protein with ferrous or ferric. But there is no iron in force field. What > is easiest way to do it? Can I just add a few lines to aminocids.rtp, like > this? > > [FE] > > [ atoms] > > FE FE 3.0000 0 > > [ bonds] > > [ angles ] > > [ impropers ] > > [ dihedrals ] > > > Thanks! > Guangyu > -- > 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.
