[gmx-users] Elastic network model

[Mark Abraham]

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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>