I turned off all non bonded interaction using the following:
energygrp_excl = SOL SOL SOL Protein_A SOL Protein_B Protein_A Protein_B
(where Protein_A and Protein_B, are the 2 molecules (peptides) in the box)
I assume this will not affect excluded volume i.e I do not expect to see
distances less that twice the radius of an atom.
However, after my simulation I get the ff result for the distance between 2
alpha C atoms in Protein_A and Protein_B (using g_dist):
0.182811
0.221014
0.240868
0.279282
0.322291
0.334325
0.356991
0.357273
0.401965
....
The diameter of a C atom is about .3nm so I was surprised to see distances less
than that.
I'll appreciate any help.
Regards
John
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