[gmx-users] non bonded interactions

[Sheyore Omovie]

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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