GROMACS version: 2020.4
GROMACS modification: No
I am trying to implement ethylene glycol (HOCH2CH2OH) into GROMACS using the TraPPE force field. The parameters for ethylene glycol can be found at the website here by going to “Try another search” on the top right of the page and then choosing “1,2-ethanediol” from the dropdown menu. Although there are parameters for the nonbonding interactions and bonds, angles, and dihedrals, my main question is based on the last bullet point of the screenshot below:
Thus, my question is as follows: How do I implement these special 1-5 intramolecular interactions using GROMACS (if it is at all possible)? In addition, will this implementation affect how I implement the standard 1-4 interactions (i.e. [ pairs ] list with gen-pairs = yes, fudgeLJ = 0, fudgeQQ = 0.5, nrexcl = 3)?
Thank you for your help.