[gmx-users] an elastic network

David L. Bostick dbostick at physics.unc.edu
Sat Oct 29 09:25:14 CEST 2005

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.

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

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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