[gmx-users] Reorienting trajectories before PCA

Bert de Groot bgroot at gwdg.de
Fri Feb 6 09:03:00 CET 2004

Chng Choon Peng wrote:
> Dear users,
>     We need to reorient and combine 2 sets of 5ns trajectories before doing
> a PCA using g_covar. We wish to show the differences on the same PC1 vs PC2
> plot.
> However, though I'm successful in extracting out the C-alpha trajectories
> using trjconv followed by concatenating the 2 Ca trajectories using trjcat,
> I'm not able to create an appropriate CA tpr file for g_covar to use.
> Gromacs provide another tool called tpbconv that is supposed to give a pure
> Ca tpx file but this option does not seem functional at this time.
> Can anyone help? Thanks!

use a .gro or .pdb for the -s option of g_covar instead of .tpr



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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