[gmx-users] an elastic network

[David]

On Sat, 2005-10-29 at 17:28 -0400, David L. Bostick wrote:
> 
> Thanks David,
> 
> 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.
This is correct, however there are only fixed lists of bonds and
exclusions. 
> 
> Sorry if this sounds wacky, but I'm just trying something out of curiosity
> :)
> 
> 
> Thanks,
> 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
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> 
> 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
> > 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
> > >
> > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> > > 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.
> > ________________________________________________________________________
> > 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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-- 
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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