Hello I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon) and also in Gromos (C6 and C12) forcefield for comparison. The original ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the original ffnonbonded.itp file in gromos**.ff listed all the pair potentials. If I change one atom potential, do I need to do anything to generate the new pair potential before running a simulation in opls-aa force field? Or how to generate the pair potentials? While for the case of gromos forcefield, the forcefield.itp file shows no pair potential will be generated. Is there any automatic ways to generate the modified LJ potentials? Should I list every possible LJ pair potentials in nonbonded.itp file? It looks like some very tedious work if several atoms are going to be modified. Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file? Values of those two are different for OPLS and Gromos.
Thanks in advance and happy new year! Best! Xueming
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