[gmx-users] PCA projections using g_anaeig

[Tsjerk Wassenaar]

Hi James,

I'm not actually sure anymore. I usually just use the projections and
combine them myself. Why not just try?

Cheers,

Tsjerk

On Wed, Jan 28, 2015 at 7:44 PM, James Starlight <jmsstarlight at gmail.com>
wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.