[gmx-users] PCA projections using g_anaeig

[Antonio Baptista]

Hi James,

Yes, but all you need are the 1D projections, since they are the 
coordinates in the PCA reference frame. So, just combine them in any way 
you want, as Tsjerk indicated. Also, keep in mind that there is actually 
no transformation of the conformation space when you do PCA, just a 
rotation of the coordinate axes.

But beware of 2D projections alone -- two different 3D distributions can 
give *exactly* the same 1-vs-2, 1-vs-3 and 2-vs-3 projections! So, if you 
want to get a better understanding of your distribution (as seems to be 
the case) try also to look at least at the 3D projection 1-vs-2-vs-3. For 
more dimensions you cannot simply "look", of course... :) And be skeptical 
about the basins you see in 2D PCA maps, since each of them typically have 
many disparate conformations lumped together. You may want to look at 
http://dx.doi.org/10.1021/jp902991u

Best,
Antonio


On Wed, 28 Jan 2015, James Starlight 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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