Re: vmd-l: connect a spring between all the atoms present in pdb structure

From: Axel Kohlmeyer (
Date: Sat Aug 04 2012 - 13:20:05 CDT

On Sat, Aug 4, 2012 at 11:31 AM, SONY kaur <> wrote:
> Hi ,
> I want to create a network model of protein in which two atoms are
> connected by springs. Generally this done in vmd by " label addspring molid
> atomid1 atomid2 k. If i want to do for entire protein , how can i do that .

two comments to that.

the label command has only analytical/visualization purposes.
for a network model like you describe, you need a simulation software.

what you describe as "spring" is a simple harmonic bond,
so the way to set this up would be through defining bonds.
however, there is a complication: you have to provide a custom
force field database, that assigns each pair of atoms a
particular and unique bondtype (or atom type combination),
so that you can have a unique equilibrium distance.

> How to store this structure with springs between atoms.

not fully automatically, but it is possible via VMD scripting.
however, before even attempting this, i strongly recommend
reading up on simulation software and looking at papers
that did similar modeling and figure out how they implemented
the model you are after.


> Thanks,
> sony,
> Ph.D student,

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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