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Sorry, I meant the repulsion term<BR><BR>
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From: omovie_johnnie@hotmail.com<BR>To: gmx-users@gromacs.org<BR>Subject: RE: [gmx-users] non bonded interactions<BR>Date: Sun, 10 Feb 2008 10:03:20 -0500<BR><BR>
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Hi Xavier,<BR>I get your point. Perhaps I should just state what I want to do.<BR>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.<BR><BR><BR>> From: X.Periole@rug.nl<BR>> Subject: Re: [gmx-users] non bonded interactions<BR>> To: gmx-users@gromacs.org<BR>> Date: Sun, 10 Feb 2008 10:24:35 +0100<BR>> <BR>> On Fri, 8 Feb 2008 20:27:35 -0500<BR>> Sheyore Omovie <omovie_johnnie@hotmail.com> wrote:<BR>> > <BR>> > I turned off all non bonded interaction using the following:<BR>> > <BR>> > energygrp_excl = SOL SOL SOL Protein_A SOL Protein_B Protein_A Protein_B<BR>> > <BR>> > (where Protein_A and Protein_B, are the 2 molecules (peptides) in the box)<BR>> > I assume this will not affect excluded volume i.e I do not expect to see <BR>> >distances less that twice the radius of an atom.<BR>> > However, after my simulation I get the ff result for the distance between 2 <BR>> >alpha C atoms in Protein_A and Protein_B (using g_dist):<BR>> <BR>> You have two types of interactions: bonded and non-bonded. Removing<BR>> all non-bonded interaction means that you only have bonds, angles and<BR>> dihedrals ... The vdW interactions are part of the non-bonded and they<BR>> actually define the "vdW" radius of the atoms through the LJ potential.<BR>> There is no explicit consideration of any atomic radius besides this<BR>> in classic force field with explicit solvent.<BR>> <BR>> It seem to me strange tho expect the distances to have any relation<BR>> with the radius if you remove them!<BR>> <BR>> <BR>> > <BR>> > <BR>> > <BR>> > <BR>> > <BR>> > 0.182811<BR>> > <BR>> > 0.221014<BR>> > <BR>> > 0.240868<BR>> > <BR>> > 0.279282<BR>> > <BR>> > 0.322291<BR>> > <BR>> > 0.334325<BR>> > <BR>> > 0.356991<BR>> > <BR>> > 0.357273<BR>> > <BR>> > 0.401965<BR>> > ....<BR>> > The diameter of a C atom is about .3nm so I was surprised to see distances <BR>> >less than that.<BR>> > I'll appreciate any help.<BR>> > <BR>> > Regards<BR>> > John<BR>> > <BR>> > <BR>> > <BR>> > _________________________________________________________________<BR>> > Need to know the score, the latest news, or you need your HotmailŪ-get your <BR>> >"fix".<BR>> > http://www.msnmobilefix.com/Default.aspx<BR>> <BR>> -----------------------------------------------------<BR>> XAvier Periole - PhD<BR>> <BR>> NMR & Molecular Dynamics Group<BR>> University of Groningen<BR>> The Netherlands<BR>> http://md.chem.rug.nl/~periole<BR>> -----------------------------------------------------<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR><BR>
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