[gmx-users] Reorienting trajectories before PCA

Chng Choon Peng cpchng at bii.a-star.edu.sg
Fri Feb 6 03:16:01 CET 2004

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

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!

Choon Peng

Mr. Choon-Peng CHNG
Research Associate
BioInformatics Institute, BMSI, A*STAR
30 Biopolis Street
#07-01 Matrix Building
Singapore 138671
Tel (O): +65 64788301 Fax (O): +65 64789047

More information about the gromacs.org_gmx-users mailing list