[gmx-users] visualize normal mode

[Anton Feenstra]

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

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|