[gmx-users] grompp and nonbonded interactions

[David L. Bostick]

Hello, I have some questions on how grompp builds nonbonded interactions.

1) when the charge on an atom type is specified by a given ff.itp file,
will the charge placed on an atom given in a molecule.itp file take
precedence?  for example, with

#include ffgmx.itp
#include molecule.itp

if the charge on a particular atom in the molecule.itp file is different
from the ffgmx.itp file, which file will the atom's charge be taken from.

2) if gen-pairs is set to yes (and fudgeQQ=fudgeLJ=0.5 for example) under
[defaults] and a molecule.itp file specifies [pairtypes] and [pairs], will
fudgeQQ be taken as 0.5 for 1-4 electrostatics while the fudgeLJ=0.5 is
overridden by the 1-4 LJ interactions specified in [pairtypes] and [pairs]?
In other words, can fudgeLJ be overridden by [pairtypes] even when
gen-pairs is set to yes?

David