[gmx-users] 1-4 LJ interactions

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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