[gmx-users] Re: dPCA
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 19 09:01:38 CEST 2005
On Tue, 2005-10-18 at 14:25 -0700, Gia Maisuradze wrote:
> Dear David,
> Thanks for your reply. I have seen -or option in Gromacs 3.3 RC2 version and
> made a trajectory file from g_angle. Then I have generated new topology file
> (tpr) for dihedral angles by using tpbconv. After that I used trr (obtained
> from g_angle) and tpr (obtained from tpbconv) and angle.ndx (obtained from
> mk_angndx) in g_covar to get eigenvactors and eigenvalues, and I got
> Segmentation fault. When I was creating all these files I was asked which
> group of dihedrals I want to include, I have picked one of them for all
> files (I don't know the comand which can include all groups).
You probably have to make your own index file for g_angle containing all
phi and psi dihedrals in the order you wish. Then you have to create a
tpr file containing (2*N)/3 atoms, where N is the number of dihedrals.
Since there are two values stored per dihedral, there will be 2*N
entries, but since atoms always have three coordinates the number is
rounded up. So for 8 dihedrals, you have 16 values which is rounded up
to 18 to make a multiple of three. You then need a tpr file with 6
> I don't know why I got segmentation fault, any idea? Could it be related to
> index file?
> Thanks in advance,
> ----- Original Message -----
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: <gmx-users at gromacs.org>
> Sent: Monday, October 17, 2005 10:29 PM
> Subject: [gmx-users] Re: dPCA
> > 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
> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >
> >> >
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