[gmx-users] non bonded interactions

[Xavier Periole]

On Fri, 8 Feb 2008 20:27:35 -0500
  Sheyore Omovie <omovie_johnnie at hotmail.com> wrote:
> 
> 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):

You have two types of interactions: bonded and non-bonded. Removing
all non-bonded interaction means that you only have bonds, angles and
dihedrals ... The vdW interactions are part of the non-bonded and they
actually define the "vdW" radius of the atoms through the LJ potential.
There is no explicit consideration of any atomic radius besides this
in classic force field with explicit solvent.

It seem to me strange tho expect the distances to have any relation
with the radius if you remove them!


> 
> 
> 
> 
> 
> 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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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------