[gmx-users] Compare NMA on CHARMM and GROMACS

Bert de Groot bgroot at gwdg.de
Thu Jan 15 09:09:00 CET 2004

¤è ¤[»¨ wrote:
> Dear all¡G
> I wanna compare NMA results on CHARMM and GROMACS¡AAs you know¡A
> NMA on CHARMM can display vibrational frequencies and average
> fluctuations of protein residues¡CBut I don't know how to comeplte
> this analysis on GROMACS¡Aeven if I've completed g_nmeig calculation
> and diagonalized Hessian matrix¡C

the frequencies are in your eigenvalues file (default: eigenval.xvg, check
the units, this was discussed in the list some time ago). Individual mode
displacements can be displayed with g_amaeig -disp.
You may also want to try g_nmens, which generates an ensemble of structures
along a selection of normal modes at a predefined temperature. This ensemble
can then be analysed with the usual g_* programs (e.g. g_rmsf for fluctuations).



ATTENTION: Please note new phone/fax numbers below!

Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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