[gmx-users] Elastic network model

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 30 11:48:32 CEST 2012

Hi Mohan,

Elastic network modeling consists of building a Hessian matrix based
on the distances. That matrix is then diagonalized and the modes are
further investigated. You could write a script to generate a .top file
with a [ bonds ] section, capturing the elastic bonds, and then use
Gromacs to generate the Hessian using the nm integrator. But that
seems more trouble than it's worth. If you think of building such a
model and then simulate it using an md integrator, be warned that
these models are very incomplete and are intended to only capture the
tangents around the starting structure.

Hope it helps,


On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena
<maruthi.sena at gmail.com> wrote:
> Hi all,
>              Can any one suggest me how to build elastic network model
> in gromacs.
> Thanks,
> Mohan
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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