[gmx-users] PCA analysis results

[Tsjerk Wassenaar]

Hi Nithyanan,

How did you preprocess the trajectory? Did you cluster and/or make
everything whole?

By the way, 50 ns is probably too short for a protein of that size. It will
probably still be relaxing and the eigenvectors will be those of the
relaxation.

Cheers,

Tsjerk

On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai <nithyanny90 at gmail.com>
wrote:

> Dear GROMACS users,
>
> I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff in
> explicit water in the cubic box with 2fs time step.
>
> I have  used g_covar and g_anaeig to perform Principal Component Analysis/
> Essential Dynamics analysis.
>
>
> But when I view the animation of the trajectory it, the movement of the
> protein looks weird.
>
> Can anyone please help to explain to me what I can do to get the right
> trajectory?
>
> Link for eigenvalue file:
>
>
>
> https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing
>
> I have used the following command line to extract the results:
>
>
> g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v
> ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig
> ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt mono_wild_filt1.pdb
> -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100
>
> pdb file link:
>
>
> https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing
>
>  g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v
> ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig
> ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr
> mono_wild_extreme1.pdb  -first 1 -last 1 -nframes 50
>
> pdb file link:
>
> https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.