I am using acpype on my system (which includes a ligand that I parametrized with gaff2/abcg2) to convert it from amber file formats to GROMACS-compatible files. In amber, I made some manual edits to the ligand dihedrals to go along with literature values, so I checked the dihedrals again after using acpype and saw that they were all multiplied by 4.184, effectively converting the dihedral barriers from kJ/mol in amber to kcal/mol in GROMACS. I wondered if GROMACS just passes in kcal/mol values for calculating dihedrals, but saw in the GROMACS documentation: “Note: Mind the conversion from kcal mol−1 for literature OPLS and RB parameters to kJ mol−1 in GROMACS.” However, I saw in the setProperDihedralsCoef function in acpype that there was a comment about this multiplication by 4.184 “Coefficients ready for GMX (multiplied by 4.184)”.
This was the command I used to run acpype:
acpype -p system.prmtop -x system.rst7 -c user -d
I just wanted to follow up to understand why this conversion occurs, if GROMACS uses kJ/mol as the documentation suggests.