[gmx-users] 1,4-interactions and pairs...again

Javier Cerezo jcb1 at um.es
Wed Jan 16 09:46:23 CET 2013

With no [pairs] section, no 1-4 interactions are computed. Note that 
gen-pairs=yes does not automatically identifies and add the 1-4 pairs in 
your system, you need to specify them in the [pair] in your topology.

[pairtypes] contain the parameters to build the potential terms for the 
pairs included in the topology. It works in a similar way as bonds, 
angles... For each pair listed, grompp look up [pairtypes] to identify 
the parameters of the 1-4 interactions, if any pair is not present in 
pairtype directive, an error will come up if gen-pair=no.
With "gen-pair=yes" the potential terms for pairs in the topology which 
are not under pairtypes are derived using addition rules and fudges.


El 15/01/13 23:00, Robson da Silva escribió:
> Hi gmx users, I'm writing a MD code and, comparing with gromacs, I have
> some doubts. When I put gen-pairs=yes, fudges=0.5 and no [pairs] or
> [pairtypes] directives, the program (gmx) would generate 1,4 pairs with the
> parameters described in the [atomtypes] directive, right? But, at the end
> of the simulation, I don't see any coul-1,4 or LJ1,4 energy values in the
> .log file. The 1,4 pairs were generated in this case?
> Thanks.

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