[gmx-users] 1-4 LJ interactions

[Andrey Gurtovenko]

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?


with kind regards,

Andrey Gurtovenko