[gmx-users] PCA

[Tsjerk Wassenaar]

Ah, so, right, you'll have to extract a trajectory for each peptide
and concatenate those trajectories.

Sorry for misreading...

Tsjerk

On Thu, Oct 18, 2012 at 9:44 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Tuba,
>
> You can concatenate the trajectories with trjcat and perform PCA on
> the resulting trajectory.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Oct 18, 2012 at 9:07 AM, Tuba Kilinc <tkilinc at gmail.com> wrote:
>> hi all,
>>
>> i would like to apply PCA (principal component analysis) for my peptides
>> that i simulated. i do know PCA for one trajectory but what if i have more
>> than one peptide ? how can i apply pca for example 10 peptides in a box ?
>>
>> typically, i start with a PCA on the simulation
>>  g_covar -s protein.pdb -f traj.xtc -v eigenvec.trr
>>
>> and i create projections on PCA vectors using g_anaeig.
>>
>> thanks
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada