[gmx-users] an elastic network
spoel at xray.bmc.uu.se
Sat Oct 29 10:17:18 CEST 2005
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
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 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
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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