there is no [ pairs ] field in the itp file

[samuelymei]

Hi,

I used the NPF2 ITP file from this repository for a Gromacs simulation. I noticed that the [ pairs ] section is missing, which normally defines 1–4 interactions (nonbonded interactions between the first and fourth atoms in a dihedral). Was this intentionally omitted during parameter fitting, or does the topology rely on automatic generation of 1–4 pairs from bond connectivity?

[orlandoacevedo]

In the Gromacs .top file use gen-pairs yes. GROMACS will automatically generate 1-4 Lennard-Jones parameters for atom pairs separated by 3 bonds using combination rules and the scaling factor (fudgeLJ). This is standard for force fields like OPLS. Please see an example .top in our GitHub IL.

[samuelymei]

Setting gen-pairs=yes defines how the parameters for 1-4 VDW interactions are generated. It does not generate the 1-4 interaction partners. It can be found in 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.

But anyway, since the parameters were fitted and used consistently without the 1-4 terms, it is fine. Because I am using software that automatically builds the 1-4 term from bond connectivity (which is not compatible with the GMX policy), I got incorrect results with this itp file. I am now fixing my software to make it fully compatible with GMX.