[gmx-users] Elastic network model

[mohan maruthi sena]

 Hi ,
         Thank you very  much .I will take   all these factors in to
account while building the model.

Thank you,
Mohan.

On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 30/08/2012 10:17 PM, Mark Abraham wrote:
>>
>> 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].
>
>
> On second thoughts, a sufficient network of harmonic bonds can suffice, but
> you need to embed the distance in the topology. [distance_restraints] are
> just easier because you can let the initial structure determine the
> equilibrium position. (Unless you don't want that)
>
> Mark
>
>
>>
>> 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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