[gmx-users] Questions regarding usage of the covariance analysis

James Starlight jmsstarlight at gmail.com
Sat Feb 28 19:22:00 CET 2015

Dear Gromacs users!

Here I'd to ask some methodological question regarding usage of
g_anaeig and g_shame utilities for the calculation of the principal
modes, projection of the trajectory on its plane and calculation of
the free energy landscape along it.

1) Is it possible to automatically provide some input file for each
execution of the g_anaeig consisted of the value correspond to the
group number in the index.ndx file ? Here I need to perform many
executions of the g_anaeig to calculate PCs from some atom subsets
defined in the index.ndx and I would not to chose the group manually
each time.

2) Is it possible to improve quality (resolution) of the colored free
energy diagrams made by
g_sham –f 2dproj_1_2.xvg –ls gibbs.xpm -notime
xpm2ps –f gibbs.xpm –o gibbs.eps –rainbow red

Thanks for help!


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