[gmx-users] Re: gmx-users Digest, Vol 66, Issue 174
alexander yakovenko
yakovenko_a at ukr.net
Tue Oct 27 21:38:55 CET 2009
Thank you, Tsjerk, for replay.
my commands:
g_covar_d -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -n sss.ndx -o sss_1000_eigenval.xvg -xpm sss_1000_covar.xpm -v sss_1000_eigenvec.trr -mwa -l
...
Option Filename Type Description
------------------------------------------------------------
-f sss_mdsi_1000.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-s sss_mdsi_1000.tpr Input Structure+mass(db): tpr tpb tpa gro g96
pdb
-n sss.ndx Input, Opt! Index file
-o sss_1000_eigenval.xvg Output xvgr/xmgr file
-v sss_1000_eigenvec.trr Output Full precision trajectory: trr trj
cpt
-av average.pdb Output Structure file: gro g96 pdb
-l covar.log Output Log file
-ascii covar.dat Output, Opt. Generic data file
-xpm sss_1000_covar.xpm Output, Opt! X PixMap compatible matrix file
-xpma covara.xpm Output, Opt. X PixMap compatible matrix file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]fit bool yes Fit to a reference structure
-[no]ref bool no Use the deviation from the conformation in the
structure file instead of from the average
-[no]mwa bool yes Mass-weighted covariance analysis
-last int -1 Last eigenvector to write away (-1 is till the
last)
-[no]pbc bool yes Apply corrections for periodic boundary conditions
Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
Choose a group for the least squares fit
Group 0 ( System) has 31748 elements
...
Group 20 ( active_site) has 54 elements
Select a group: 20
Selected 20: 'active_site'
Choose a group for the covariance analysis
Group 0 ( System) has 31748 elements
...
Group 20 ( active_site) has 54 elements
Select a group: 20
Selected 20: 'active_site'
Calculating the average structure ...
trn version: GMX_trn_file (double precision)
Last frame 2000 time 2000.000
Constructing covariance matrix (162x162) ...
Last frame 2000 time 2000.000
Read 2001 frames
Trace of the covariance matrix: 6.22756 (u nm^2)
100%
Diagonalizing ...
Sum of the eigenvalues: 6.22756 (u nm^2)
Writing eigenvalues to sss_1000_eigenval.xvg
Writing reference, average structure & eigenvectors 1--162 to sss_1000_eigenvec.trr
Wrote the log to covar.log
gcq#86: "Shake Barrels Of Whisky Down My Throat" (Throwing Muses)
g_anaeig_d -v sss_1000_eigenvec.trr -eig sss_1000_eigenval.xvg -v2 sss_1000_eigenvec.trr -eig2 sss_1000_eigenval.xvg -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -first 1 -last 10 -n sss.ndx -proj -over
...
Option Filename Type Description
------------------------------------------------------------
-v sss_1000_eigenvec.trr Input Full precision trajectory: trr trj
cpt
-v2 sss_1000_eigenvec.trr Input, Opt! Full precision trajectory: trr trj
cpt
-f sss_mdsi_1000.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt
-s sss_mdsi_1000.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
pdb
-n sss.ndx Input, Opt! Index file
-eig sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file
-eig2sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file
-comp eigcomp.xvg Output, Opt. xvgr/xmgr file
-rmsf eigrmsf.xvg Output, Opt. xvgr/xmgr file
-proj proj.xvg Output, Opt! xvgr/xmgr file
-2d 2dproj.xvg Output, Opt. xvgr/xmgr file
-3d 3dproj.pdb Output, Opt. Structure file: gro g96 pdb
-filt filtered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-extr extreme.pdb Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-over overlap.xvg Output, Opt! xvgr/xmgr file
-inpr inprod.xpm Output, Opt. X PixMap compatible matrix file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-first int 1 First eigenvector for analysis (-1 is select)
-last int 10 Last eigenvector for analysis (-1 is till the
last)
-skip int 1 Only analyse every nr-th frame
-max real 0 Maximum for projection of the eigenvector on the
average structure, max=0 gives the extremes
-nframes int 2 Number of frames for the extremes output
-[no]split bool no Split eigenvector projections where time is zero
-[no]entropy bool no Compute entropy according to the Quasiharmonic
formula or Schlitter's method.
-temp real 298.15 Temperature for entropy calculations
-nevskip int 6 Number of eigenvalues to skip when computing the
entropy due to the quasi harmonic approximation.
When you do a rotational and/or translational fit
prior to the covariance analysis, you get 3 or 6
eigenvalues that are very close to zero, and
which should not be taken into account when
computing the entropy.
trn version: GMX_trn_file (double precision)
Read mass weighted reference structure with 54 atoms from sss_1000_eigenvec.trr
Read mass weighted average/minimum structure with 54 atoms from sss_1000_eigenvec.trr
Read 162 eigenvectors (for 54 atoms)
Read 162 eigenvalues from sss_1000_eigenval.xvg
Read mass weighted reference structure with 54 atoms from sss_1000_eigenvec.trr
Read mass weighted average/minimum structure with 54 atoms from sss_1000_eigenvec.trr
Read 162 eigenvectors (for 54 atoms)
Read 162 eigenvalues from sss_1000_eigenval.xvg
Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
Note: the structure in sss_mdsi_1000.tpr should be the same
as the one used for the fit in g_covar
Select the index group that was used for the least squares fit in g_covar
Group 0 ( System) has 31748 elements
...
Group 20 ( active_site) has 54 elements
Select a group: 20
Selected 20: 'active_site'
Select an index group of 54 elements that corresponds to the eigenvectors
Group 0 ( System) has 31748 elements
...
Group 20 ( active_site) has 54 elements
Select a group: 20
Selected 20: 'active_site'
RMSD (without fit) between the two average structures: 0.000 (nm)
10 eigenvectors selected for output: 1 2 3 4 5 6 7 8 9 10
Last frame 2000 time 2000.000
Calculating overlap between eigenvectors of set 2 with eigenvectors
1 2 3 4 5 6 7 8 9 10
Will compare the covariance matrices using 162 dimensions
Trace of the two matrices: 6.22756 and 6.22756
Square root of the traces: 2.49551 and 2.49551
The overlap of the covariance matrices:
normalized: 1.000
shape: 1.000
gcq#334: "Aber wenn der Quarterback kommt, um dir die Brille abzunehmen Sag ihm: Danke die bleibt wo sie ist" (Wir sind Helden)
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] nans in g_anaeig
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<8ff898150910271319n5a10949aq13298eebb119c635 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Alex,
Can you paste the actual sequence of commands you used?
Cheers,
Tsjerk
2009/10/27 alexander yakovenko <yakovenko_a at ukr.net>:
> Hi all!
> I run into a problem trying to project trajectory on the eigenvector(s)
> (with g_anaeig -proj ) from covariace matrix - all projections are nan. The
> eigenvalues are OK, the g_anaeig -comp -v2 -eig2 -over options works OK so
> eigenvectors seems are OK (but g_anaeig -2d fails to nan too). I am using
> gromacs-4.0.5 on x86-64 CentOS5 (compiled with gcc-34).
> What can help me to project it properly?
> Regards,
> Alex.
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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End of gmx-users Digest, Vol 66, Issue 174
******************************************
Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
03143
acad.Zabolotnogo str. 150
Kiev
Ukraine
______________________________________________
E-mail: yakovenko_a at ukr.net
Хочешь стать успешным? Получи настоящий британский MBA – mba-ukraine.com .
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