[gmx-users] non bonded interactions

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Feb 9 18:37:40 CET 2008

Quoting: "The diameter of a C atom is about .3nm so I was surprised to see
distances less than that."

You mean the diameter (radius) as set in vdwradii.dat? This means  
nothing to mdrun, only special tools like genbox.

energygrp_excl allows you to define:
"Pairs of energy groups for which all non-bonded interactions are excluded"

And if there are no non-bonded interactions between proteinA and  
proteinB, then why would they not get closer than 3A? Why would you  
ever run md like this? I could understand your concern if you were  
talking about an mdrun -rerun setup, but you didn't mention that so I  
assume that you are not.

Bottom line is that what you are getting is expected. Since you seem  
to not want this result then you should reconsider your use of  


-- original message --

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):









The diameter of a C atom is about .3nm so I was surprised to see  
distances less than that.
I'll appreciate any help.


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