[gmx-users] non bonded interactions

[chris.neale at utoronto.ca]

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  
energygrp_excl.

Chris.

-- 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):






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