[gmx-users] PCA analysis results

[Tsjerk Wassenaar]

Hi Nithyanan,

Right. So now we have that clear, I've had a look at the PDB file :p
What you see is the result of filtering over a single eigenvector. You
protein is kind of curling up through rotations of domains. You can't
describe these rotations with a single eigenvector. They will be dispersed
over multiple, and you will need at least two to capture the rotations.
Maybe there's a twist associated and then you'd surely need one more.

As an aside, looking at the trajectory confirms me that this is a
relaxation motion. I don't know whether you removed a ligand and this is a
functional relaxation, or that is was started from a crystal structure, but
it is something to be aware of.

Hope it helps,

Tsjerk

On Fri, Dec 18, 2015 at 8:51 PM, Nithyanan Annamalai <nithyanny90 at gmail.com>
wrote:

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