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.
Javier
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.
--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434
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