[gmx-users] Elastic network model

[mohan maruthi sena]

Hi,
     Thanks for a quick reply. In these models we use a distance
cut-off method. Around a particular atom we take a cut-off distance
and connect to all those atoms which fall in the cut-off. I do not
understand, how to connect this atoms with the other atoms falling in
cut-off distance. I have written a script to know the atom numbers
falling with in cut-off distance. I replace bonds section in topology
with these atom connectivity information that i got from script. Is
this method correct or else please suggest me a way.Can you elaborate
on "write a script to generate .top"


Thank you very much,
Mohan

On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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,
>
> Tsjerk
>
> 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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