[gmx-users] Explicit Topology Question

Mark Abraham mark.j.abraham at gmail.com
Mon Jan 9 19:39:24 CET 2017


Do you mean on the same three atoms, or that each of your beads has such
"backward" angles? I haven't looked at that code in a long time, but it's
probably pretty dumb - two bonds with a common atom generate an angle, so
if you don't want the angle, don't specify redundant bonds?


On Mon, Jan 9, 2017 at 7:30 PM Thomas Allen <thomas.c.allen at rice.edu> wrote:

> Hello all,
> I'm currently implementing a simple polymer coarse-grained model in
> GROMACS through some modifications to the OPLS force field. An issue
> I'm having is that there are certain angles generated when parsing the
> topology file which I don't want. For example, assuming atoms A, B, C,
> I get the angles:
> A B +C
> and
> -C B A
> However, I only want the forward version (A B +C). I know that
> unwanted dihedrals can be excluded by topology file settings, and I
> know that CHARMM has settings which allow only certain angles or other
> interactions specified explicitly in the topology file entry to be
> generated for a given residue. I was wondering if there was an
> equivalent when using GROMACS, or if I will have to come up with some
> clever text editing to fix the issue in the topol.top file itself.
> Thanks,
> Tom Allen
> --
> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list