[gmx-users] 1-4 LJ interactions

[Andrey Gurtovenko]

Dear Justin,

thank you for the clarification.

I think my confusion is in part due to the urea topology file
used in the manual as an example, which does not contain
the [pairs] section.

with kind regards,

Andrey

On Wed, Apr 1, 2020 at 3:32 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 3/31/20 12:59 PM, Andrey Gurtovenko wrote:
> > Dear All,
> >
> > Recently I realized that I don't fully understand what should be done
> > in Gromacs to account for 1-4 LJ interactions.
> >
> > According to the manual:
> >
> > "gen-pairs is for pair generation. The default is ‘no’, i.e. get 1-4
> > parameters from the pairtypes list. When parameters are not present in
> > the list, stop with a fatal error. Setting ‘yes’ generates 1-4
> > parameters that are not present in the pair list from normal
> > Lennard-Jones parameters using fudgeLJ."
> >
> > http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html
> >
> > Therefore, I had an impression that to account for 1-4 interactions in
> > some generic force-field, it is enough to
> > set gen-pairs=yes.
> >
> > However, it turns out that this is not the case:
> > in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the
> > [pairs] section of the topology file of a system.
> > Otherwise 1-4 interactions are NOT accounted for.
> >
> > Can someone comment on this?
> > If I am right, maybe it is worth to clarify this point in the manual?
>
> The language in the manual is correct, either pair *parameters* are
> generated, or they are not. The topology is different from the
> parameters; if *interactions* are not there, then nothing is done.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
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