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

James Starlight jmsstarlight at gmail.com
Sat Feb 28 19:27:23 CET 2015

just forgot to ask

3) how it will be possible to mark on the projections as well as on
the free energy landscapes points corresponded to the initial and
final conformations along the trajectory?

2015-02-28 19:21 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> 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!
> James

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