[gmx-users] custom topology questions

[Eric Smoll]

Hello Gromacs Users,

I have a few custom topology questions. Input on any of these questions
would be greatly appreciated.

1.) What gromacs tools use the information in atomtypes.atp?

2.) Table 5.4 claims the atomtypes directive consists of lines with the
format:
atom-type, mass, charge, particle-type, V-parameter, W-parameter
in the opls-aa directory, ffnonbonded.itp has:
atom-type, bond-type, atomic-number, mass, charge, particle-type,
V-parameter, W-parameter
Is it OK to use either format safely? Gromacs isn't hardcoded to use a
special format for the opls-aa directory, correct?

3.) consider "configuration A":
gen-pairs is set to yes, fudge-LJ to 0.5, and fudgeQQ to 0.5, and a "pairs"
directive is provided with two atom-numbers per line. I expect this
configuration will calculate scaled 1-4 interactions (LJ and coulomb) and
apply them to all the atom-number-pairs listed in the "pairs" directive.
Now consider "configuration B":
gen-pairs is set to yes, fudge-LJ to 0.5, and fudgeQQ to 0.5, and a "pairs"
directive is provided with two atom-numbers, a "1" for the function type,
an X-parameter, and a Y-parameter for every line.
Am I correct in assuming the gen-pairs and fudgeLJ do nothing here? Am I
correct in assuming that fudgeQQ is still applied to 1-4 coulomb
interactions? When parameters are provided in the "pairs" directive, they
only apply to LJ-type interactions, correct (i.e., the only way to tune 1-4
coulomb interactions is with the fudgeQQ factor)?

4.) In the "dihedrals" directive, can the user specify a type-1 dihedral
("proper dihedral") repeatedly to form a superposition potential or do
later parameters override previous parameters. For example,
[ dihedrals ]
;i   j   k   l   function-type   phi_s, k_phi, multiplicity
1 2 3 4 1 0 1 1; (1 + cos(phi))
1 2 3 4 1 0 1 1; (1 + cos(phi))
1 2 3 4 1 0 1 1; (1 + cos(phi))
to yield a potential equivalent to 3*(1 + cos(phi)) or (1 + cos(phi))?

Thank you!

Best,
Eric