[gmx-users] Re: dPCA

[Mu Yuguang (Dr)]

Dear Gia,
You are welcome. In the last email I made something wrong. The program I
sent to you will read a trajectory file having the format:
Time  phi1  psi1 phi2 psi2 .....
The program itself calculates cos and sin. 

Dr. Yuguang Mu
Division of Structural and Computational Biology
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive 
Singapore 637551
Tel: 63162885
Fax: 67913856
 

-----Original Message-----
From: Gia Maisuradze [mailto:gia at chem.unr.edu] 
Sent: Friday, October 14, 2005 10:49 AM
To: Mu Yuguang (Dr); Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: dPCA

Dear Yuguang,

Thanks for your email and program. I think it is very interesting to
find 
out how good is dPCA, and where we can see a noticeable discrepancy
between 
dPCA and normal PCA. My first impression was that the noticeable
difference 
in results can be observed for small systems, for big proteins they
should 
be similar (or close to each other). However, more detail studies are 
necessary to make some conclusions.

Gia

----- Original Message ----- 
From: "Mu Yuguang (Dr)" <YGMu at ntu.edu.sg>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>; "Gia 
Maisuradze" <gia at chem.unr.edu>
Sent: Thursday, October 13, 2005 6:41 PM
Subject: RE: [gmx-users] Re: dPCA


Dear Gia, David,
I think in some cases dPCA definitely better then normal PCA, as our
paper (Proteins) described. One shortcoming of it is that just like the
NMR structure determination, only the short range parameters (dihedrals)
involved. So for big proteins some important global motions may be mixed
or equally weighted with local motions.
I do not believe the many minima shown by dPCA are artifacts.

Gia, sorry to reply your requests late.
Here also send you the fortran program I used for dPCA analysis.
Similarly as David said, it read a trajectory file with the format
time cos(a1) sin(a1) cos(a2) sin(a2) ....

In case you want compare.


Dr. Yuguang Mu
Division of Structural and Computational Biology
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive
Singapore 637551
Tel: 63162885
Fax: 67913856

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David
Sent: Friday, October 14, 2005 4:45 AM
To: Gia Maisuradze
Cc: gmx-users at gromacs.org
Subject: [gmx-users] Re: dPCA

On Thu, 2005-10-13 at 13:36 -0700, Gia Maisuradze wrote:
> David,
>
> Thank you very much for your reply. As you said, dPCA shows more
minima and
> free energy landscape is more rugged than in "normal" PCA. According
to the
> paper that I mentioned in my previous email, dPCA is more realistic,
and
> Cartesian PCA represents an artifacts due to the mixing of internal
and
> overall motion. On the other hand, there are other opinions, for
example
> Erik Lindahl mentioned that the resulting eigenvectors are no longer
> orthogonal in the cartesian norm and dPCA is problematic.
>
> I am going to test dPCA and compare the results to normal PCA. Maybe
it can
> clarify some problems.

We are currently considering some other possibilities as well. A recent
paper by the Levy group used PCA on a set of internal distances (e.g.
Ca-Ca) which has the advantage that you don't need to do a LSQ
superposition, but also that long distances weigh differently than short
distances. A problem in any method is that even if you obtain orthogonal
eigenvectors they may still be coupled. If you find a general solution
for these problems it may be very useful indeed.

>
> With best wishes,
>
> Gia
>
> ----- Original Message ----- 
> From: "David" <spoel at xray.bmc.uu.se>
> To: "Gia Maisuradze" <gia at chem.unr.edu>
> Cc: <gmx-users at gromacs.org>
> Sent: Thursday, October 13, 2005 1:03 PM
> Subject: Re: dPCA
>
>
> > On Thu, 2005-10-13 at 11:48 -0700, Gia Maisuradze wrote:
> >> Dear David,
> >>
> >> I have checked the changes in new Gromacs 3.3. It says that
dihedral
> >> PCA is supported in g_angle (you are the author). Does it mean that
we
> >> can do dihedral principal component analysis for proteins? Is it
the
> >> same type of analysis that has been done by Gerhard Stock' group
> >> (PROTEINS, 58, 45, 2005)? If yes, I don't clearly understand how I
can
> >> do that. Normal PCA (in cartesian coordinates) can be done by using
> >> g_covar, where we build the covariance matrix and diagonalize it,
and
> >> get eigenvectors and eigenvalues. Then analyze them.
> >>
> >> Could you, please, explain how I can do dPCA on Gromacs, if it is
> >> possible.
> > Yes, you use g_angle -oc to produce a new trajectory file
containing:
> > cos(phi) sin(phi) cos(psi) sin(psi) etc.
> > This you run through g_covar.
> >
> > According to some people this information is not really useful for
> > protein analysis, as it can show many false minima and it is hard to
go
> > back to real space. Barriers you see may be trivial due to
overlapping
> > atoms.
> >
> >
> >>
> >> The same question I have asked Erik Lindahl, but he did not know
about
> >> dPCA in new Gromacs version.
> >>
> >> Thanks,
> >>
> >> Gia
> > -- 
> > David.
> >
________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org
http://xray.bmc.uu.se/~spoel
> >
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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