[gmx-users] user defined potential(repulsive) for atoms falling with in three residues
mohan maruthi sena
maruthi.sena at gmail.com
Wed May 16 21:23:47 CEST 2012
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
E(rep)= epsilon (sigma/rij)^12
Please let me know how I can implement this in Gromacs.
Thanks and Regards,
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