[gmx-users] RE: Normal mode analysis

[Maria Musgaard]

If you want to generate a kind of trajectory from the eigenvectors, I  
think you can use g_nmtraj and then visualise the vibration with e.g.  
VMD.

/Maria


Quoting Marudachalam S <msundaram at ncbs.res.in>:

> I don't know what exactly you are looking for, but normal modes can be
> visualized by freewares like Chemcraft, Molekel, etc. Hope it helps.
>
> Marudachalam.
>
>>
>> ________________________________________
>>
>> Hi All,
>>          I am doing normal mode analysis. After getting the eigen
>> frequencies, is there a way we can visualize the vibrational
>> modes in gromacs. And even how to know which frequency
>> corresponds to which mode of vibration. I saw that IED is used to
>> visualize normal modes by integrating it with VMD. But I
>> installed VMD on my windows machine. So I dont think there is a
>> way to install IED on windows. Please let me if there are any
>> softwares which can visualize normal modes if so, how to get
>> them?
>>
>> Thank you
>> abhigna
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>
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