[gmx-users] an elastic network

David 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
> 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
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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

More information about the gromacs.org_gmx-users mailing list