[gmx-users] Re: dPCA

[David van der Spoel]

On Mon, 2005-10-17 at 17:51 -0700, Gia Maisuradze wrote:
> David,
> 
> 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 
> like:
> [ 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,
> 
> 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >