Hello all, I am trying to understand the topology file for gromacs. so as to make n-alkane chain. for that I have dihedral parameters of periodic type. In the manual it says that
With the periodic GROMOS (dihedral ) potential a special 1-4 LJ-interaction must be included; for this reason I set gen-pairs = yes in [default] in [molecule type] name nrexcl=2 (to take in to account 1-4 interaction) and then again in [pairs], I list down all 1-4 pairs, I am wondering is it correct to do all three, or I am missing something. thanks in advance, I appreciate your reply, Amit Jain
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