GROMACS version: 2018
GROMACS modification: No
I was wondering how intramolecular electrostatic interactions are treated as a default in gromacs, i.e. which interactions are excluded and which included by default? I am mostly concerned with small molecule in solvent MD simulations and extracting electrostatic forces of solvents with the solute’s functional groups, or between functional groups within different parts of the solute (parts which are far apart, i.e. 10 bonds or so).
Also, I’d be interested in any general recommendations how to treat such intramolecular electrostatics “properly”.
Thanks in advance for the advice.
nrexcl for all biomolecular force fields is 3, meaning that everything within 3 bonds is excluded and 1-4 interactions are treated with a force field-specific scaling factor. These are listed in the
[defaults] directive of each force field.
Any intramolecular interaction that is further than 3 bonds apart is treated like a normal nonbonded interaction.
Do whatever is consistent with the parent force field for which you are developing the molecule’s topology.
One follow up question:
So, is it correct that the [ pairs ] part in my MD parameters of my solute (obtained using Antechamber) specifies exactly those 1-4 and farther interactions? I’m asking since I’ve only found [ pairs_nb ] described when searching for this in the manual.