Sorry, I meant the repulsion term
From: [EMAIL PROTECTED]: [EMAIL PROTECTED]: RE: [gmx-users] non bonded
interactionsDate: Sun, 10 Feb 2008 10:03:20 -0500
Hi Xavier,I get your point. Perhaps I should just state what I want to do.I am
trying to get a no interaction reference state for my main simulation. i.e
wherein the atoms will behave like ideal gas spheres (excluded volume would not
be affected). leaving the dispersion term in vdw and turning off all other non
bonded may accomplished this, I guess this is not possible.> From: [EMAIL
PROTECTED]> Subject: Re: [gmx-users] non bonded interactions> To:
[email protected]> Date: Sun, 10 Feb 2008 10:24:35 +0100> > On Fri, 8 Feb
2008 20:27:35 -0500> Sheyore Omovie <[EMAIL PROTECTED]> 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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know the score, the latest news, or you need your Hotmail®-get your > >"fix".>
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-----------------------------------------------------> XAvier Periole - PhD> >
NMR & Molecular Dynamics Group> University of Groningen> The Netherlands>
http://md.chem.rug.nl/~periole>
----------------------------------------------------->
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