[gmx-users] Elastic network model

[Tsjerk Wassenaar]

Hi Mohan,

You need to check chapter 5 of the gromacs manual to understand the
topology format to write. You probably need only to define one atom
type and the C6/C12 parameters could probably even be set to zero. You
need to write an [ atoms ] section, and a [ bonds ] section, according
to the specifications in the manual.

Cheers,

Tsjerk

On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena
<maruthi.sena at gmail.com> wrote:
> 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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-- 
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