[gmx-users] an elastic network
David L. Bostick
dbostick at physics.unc.edu
Sat Oct 29 23:28:29 CEST 2005
Sorry if I wasn't clear. I wanted to treat a mesh of particles whose
interparticle interactions are solely harmonic. I want to draw a harmonic
bond between any 2 particles in the mesh if they are some distance, R,
apart. Thus the resulting forcefield will have its energy minimum at the
initial configuration of the mesh. It sounds like from your answer, that as
long as any particle in the mesh has less than 32 harmonic bonds to any
other particle, there can be an exclusion between the particles. If this is
right then I am satisfied.
Sorry if this sounds wacky, but I'm just trying something out of curiosity
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On Sat, 29 Oct 2005, David wrote:
> 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
> > 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
> > 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
> > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> > David Bostick Office: 262 Venable Hall
> > Dept. of Physics and Astronomy Phone: (919)962-0165
> > Program in Molecular and Cellular Biophysics
> > UNC-Chapel Hill
> > CB #3255 Phillips Hall dbostick at physics.unc.edu
> > Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
> > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
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> 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
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