[gmx-users] Explicit Topology Question

[Mark Abraham]

Hi,

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?

Mark

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
>
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