[gmx-users] Re: dPCA
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 18 07:29:26 CEST 2005
On Mon, 2005-10-17 at 17:51 -0700, Gia Maisuradze wrote:
> I have tried to do dPCA on Gromacs 3.3 RC2. First, I have generated
> angle.ndx by using mk_angndx where in option -type I wrote dihedral,
> ryckaert-bellemans or phi-psi option does not work. So my angle.ndx looks
> [ Phi=180.0_2_7.11 ]
> 1 2 4 5
> [ Phi=180.0_2_33.5 ]
> 2 4 6 8 8 10 12 14 14 16 18 20
> [ Phi=180.0_6_1 ]
> 4 6 7 9 10 12 14 16 16 18 20 22
> [ Phi=0.0_2_2.09 ]
> 5 4 6 8
> [ Phi=0.0_0_0 ]
> 7 6 8 9 19 20 22 23 20 22 25 24
> 20 22 25 26
> [ Phi=0.0_6_1 ]
> 6 8 10 12 12 14 16 18
> then I used angle.ndx along with trajectory and tpr files to produce
> trajectory file for dPCA. In g_angle I wrote for -type option dihedral. Also
> it asks the group to choose, each group has a different number of elements.
> Which one to pick? I found that -oc calculates dihedral autocorrelation
> function. My concern is I could not produce cos(phi) sin(phi) cos(psi)
> sin(psi), as we discussed in our one of the previous emails. Also, the
> dihedral autocorrelation function that I got from -oc option is in xvg
> format, for g_covar I need either xtc or trr format.
> Are steps described above correct to perform dPCA? Does Gromacs 3.3 RC2
> support dPCA?
Use the -h option then you will see that you need -or
The index file you may need to make yourself.
Please put further questions on the mailing list.
> Thanks in advance,
> ----- 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users