[gmx-users] RE: Normal mode analysis

[minnu vijayan]

hi all
i am a new user of gromacs. tried to run normal mode analysis. but failed. i
did up to mdrun.but in output i am not getting .mtx file.(hesian matrix)
what may be the problem..can anybody help regarding this?

On Fri, Nov 21, 2008 at 8:01 PM, Maria Musgaard <musgaard at chem.au.dk> wrote:

> 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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