GROMACS version:2020
GROMACS modification: No
Hi,
I have parametrised my small molecule using Glycam06 in amber and used ACPYPE to generate a gromacs topoology file.
Gen-pairs is turned off, the nrexcl is 3 and extra Lennard-Jones and electrostatic interactions between pairs have been added in the [ pairs_nb ] section with function 1.
As it says in the documentation, " Energies for [ pairs_nb ] are added to the “LJ-(SR)” and “Coulomb-(SR)” terms."
I was wondering whether there was a way to update the topology file in order to separate the LJ-14 and Coulomb-14 energies from the “LJ-(SR)” and “Coulomb-(SR)” terms in the output or not?
Furthermore, how does the different way of outputting the LJ 14 and Coulomb 14 energies based on how the pairs are described in the topology files affect a md simulation that contains a protein described with [ pairs ] and type 1 or type 2 and a small molecule that is described as mentioned above? Would that not make the SR values quite complicated with the 1-4 interaction energies of the small molecule included and those of the protein not?