[gmx-users] Elastic network model

[Mark Abraham]

On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
> Hi,
>          I am going through it , i will understand it  and try to build
> the topology.

Fundamentally, harmonic bonds do not serve your purpose, since you need 
an interaction that is harmonic in the change in distance, not harmonic 
in the distance. Hence your problems with collapsing systems. As such, 
you want to look at using distance restraints, rather than [bonds].

Mark

> 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
>> --
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