Hi all, I am using a user defined potential to describe non-bonded interactions, which describes attractive potential for residues separated by four or more bonds . Now I want to describe a user defined potential(repulsive) for atoms falling with in three residues and which are not determined to be attractive, as I tried to elaborate below:
condition 1: if the two atoms are separated by four or more bonds i use attractive LJ potential. condition 2: if two atoms are not determined to be attractive or fall with in three bonds of each other(i, i+3) then their interaction is defined by repulsive term: E(rep)= epsilon (sigma/rij)^12 Please let me know how I can implement this in Gromacs. Thanks and Regards, Mohan
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