[gmx-users] visualize normal mode

[Lianqing Zheng]

Sorry, this is quite a time ago.

I tried this commend:

g_anaeig_d -last 63 -first 63 -extr extreme.pdb  -nframes 10 -s nm.tpr

However, I then got an error of not finding traj.xtc file. How can I get
this traj.xtc file? I tried to add -x traj.xtc in the cg and nm runs, but
there was no such output.

Thanks!

Lianqing


On Thu, 16 Jun 2005, Anton Feenstra wrote:

>Lianqing Zheng wrote:
>
>> Dear gmx-pals,
>> 
>> I'm wondering if there is any visualization tool to watch the movement of
>> each vibrational mode after I get the frequencies and eigenvectors from
>> gmx, just like Molden visualizes Gaussian's freq calculations.
>
>g_anaeig lets jou project coordinates along the eigenvectors in to a 
>(series of) pdb file(s). These you can view as a trajectory (with e.g. 
>VMD or ngmx), or superposed (with e.g. rasmol).
>
>-- 
>Groetjes,
>
>Anton
>
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