[gmx-users] Double-well potential for bonded interaction

[John Whittaker]

Hi Jacek,

Gromacs allows for the implementation of any kind of bonded interaction
through user-defined tabulated functions. You'll have to build a table for
it, but it's definitely more straightforward than messing around with
restraints.

Check out section 4.2.14 of the manual: "Tabulated bonded interaction
functions".

Best,

John

> Hi,
>
> Does anybody know how to define for a specific bond a double-well
> potential?
>
> I've looking into the definitions in the gromacs manual
> (manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
> and
> manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html),
> but for now I can only imagine using bond restraints in a similar manner
> shown here for position restraints:
> manual.gromacs.org/current/reference-manual/functions/restraints.html
>
> It feels like there should be a more elegant way of doing that.
>
> Thanks for your suggestions in advance!
>
> Best,
> Jacek
>
> ________________________________________________
> Dr. Jacek Kozuch
>
> Freie Universität Berlin
> Fachbereich Physik
> Arnimallee 14
> Raum 1.1.35
> 14 195 Berlin
> ________________________________________________
>
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----------------------------------------

John Whittaker
Ph.D. Candidate
Department of Mathematics and Computer Science
Freie Universität Berlin

+49 0160 936 04221