[gmx-users] PCA analysis results

[Tsjerk Wassenaar]

Hi Nithyanan,

It's guessing a bit, as the actual answer can only be obtained by tracking
some parameters during the simulation, but I would suggest to aim for at
least 200 ns. It think the relaxation will take more time than you have, so
say until (at least) 100 ns, and then you need to have enough sampling to
characterize the dynamics after relaxation.

Cheers,

Tsjerk

On Fri, Dec 18, 2015 at 9:14 PM, Nithyanan Annamalai <nithyanny90 at gmail.com>
wrote:

> Dr Tsjerk,
>
> Thank you for your explanation.
>
> The PDB model I used in this simulation was obtained from I-TASSER.
> There is no ligand involved.
>
> Dr, may I know what would be the optimal/ suggested simulation time for
> this protein with 567 aa?
>
> On Sat, Dec 19, 2015 at 4:06 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > 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.
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-- 
Tsjerk A. Wassenaar, Ph.D.