[gmx-users] Elastic Network Model

Joe Joe ilchorny at gmail.com
Wed Apr 1 03:32:11 CEST 2009

On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman <jadelman at berkeley.edu>wrote:

> I am interested in potentially using gromacs to do some calculations on an
> C-alpha based elastic network model of the protein that I'm working on. I'm
> curious if other users have done similar types of calculations, and if so,
> what protocol you used. I realize that there are a lot of webservers out
> there that do this calculation, but I want to be able to use a heterogeneous
> network of spring constants, and have a bit more flexibility than many of
> them allow. Gromacs seemed like it might be a good option for tackling this
> problem since it can calculate the Hessian and generate the normal modes
> from an arbitrary force field. it also had a bunch of nice analyses tools
> available as well.

We use the ASN server from Ivet Bahar's group and get nice results.

> Right now I am looking for suggestions on how to explicitly turn off all
> non-bonded interactions (the only FF terms are bonded terms).

Define the atom types in your top file, instead of #include ff***.itp  and
set the LJ and Q's to zero or set nrexcl to > then the number of atoms (not
exactly sure what this will do but you can give it a try)

> Is the best option to use energygrp excl? Any other useful suggestions for
> using gromacs for this purpose would also be appreciated.
> Josh
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