[gmx-users] PCA projections using g_anaeig

[James Starlight]

Thx, Tsjerk!

So normally gromacs make 2D projections  exactly only on 1 and 2 components
(even if 100 modes have been calculated for instance) doest it?

2015-01-28 16:13 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:

> Hi James,
>
> If you have the 1D projections as 1.xvg and 3.xvg:
>
> paste 1.xvg 3.xvg | awk '/^[^;&@#]/{print $2, $4}' > 2d.dat
>
> Cheers,
>
> Tsjerk
> On Jan 28, 2015 3:25 PM, "James Starlight" <jmsstarlight at gmail.com> wrote:
>
> > Dear Gromacs users!
> >
> > I'd like to ask about possibility to make projection of the MD trajectory
> > onto the subset of selected PC calculated by g-covar
> >
> >
> > e.g using
> >
> > g_anaeig –v eigenvec.trr –s md.tpr –f md.xtc –first 1 –last 3  -2d
> >
> >
> > produce projection of the md.xtc onto the 1 and 2 components although 1-3
> > modes has been calculated. How it would be possible to make the same
> graph
> > using 1 and 3rd components instead?
> >
> >
> > Thanks for help,
> >
> > James
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