[gmx-users] PCA analysis results

[Nithyanan Annamalai]

Hi Dr Tsjerk,

I didn't do any clustering or make it whole.

I just use the .xtc that I ontained after the simulation since I found out
there is no pbc effect of the protein.

On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

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