[gmx-users] an elastic network

[David]

On Sat, 2005-10-29 at 03:25 -0400, David L. Bostick wrote:
> Hello folks,
> 
> I was thinking about treating a set of particles as an "elastic" object, by
> drawing a pliable elastic network (i.e. connecting particles that are less
> than some distance, R, apart with a harmonic bond).  I have a few questions
> about some practical matters implementing this in gmx.
It's not entirely clear to me... You want only the particles within a
certain distance to be attracted? Why not just use a deep Lennard Jones
potential?

> 
> 1) If I remember correctly, isn't there a maximum number of bonded
> interactions for a single interaction detected by grompp? If so, is there a
> workaround?
> 
You're thinking of the max number of exclusions which still stands at
32.

> 2) Provided I am right on #1, I have thought of a workaround using harmonic
> distance restraints.  My question on this though, is that if I use distance
> restraints, is this interpreted as a "bonded interaction?"  That is... will
> the exclusions rule still apply? I do not wish to have the harmonically
> connected particles interact via "nonbonded" interactions, so this is an
> important issue.  I understand that I can always list the exclusions in the
> topology, but I would rather take care of them with the [ defaults ] tag in
> my topology.
> 
> 3) Is there another way that I haven't thought of?
> 
> Thanks for any help.
> 
> David
> 
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> David Bostick					Office: 262 Venable Hall
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> Program in Molecular and Cellular Biophysics
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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