[gmx-users] Elastic network model

[mohan maruthi sena]

Hi,
        I am going through it , i will understand it  and try to build
the topology.

Thank you,
Mohan

On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
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