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Bug #1510

gmx check and gmx dump do not work for tng files

Added by David van der Spoel about 5 years ago. Updated about 5 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

gmx dump -f traj2.tng shows only the molecule definition but no coordinates, etc.

Command line:
gmx dump -f traj2.tng

Molecule: trichloromethane, count: 1000
Chain:
Residue: MOL
Atom: C1 (c3)
Atom: H1 (h3)
Atom: Cl1 (cl)
Atom: Cl2 (cl)
Atom: Cl3 (cl)

gcq#22: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)

traj2.tng (249 KB) traj2.tng David van der Spoel, 05/24/2014 09:16 AM

Associated revisions

Revision 758eba66 (diff)
Added by Magnus Lundborg about 5 years ago

Bug fix in the TNG library to improve reading.

Reading single frame frame sets did not work properly.
Fixes #1502 and partial fix of #1510.

Reread frame set after getting stride length.

Extra check to avoid reading past end of file when
checking what data blocks are present.

Change-Id: I5275382bd49b5b46ebfdebe535c53d2f09015bc0

Revision 75b83417 (diff)
Added by Magnus Lundborg about 5 years ago

Fix bug writing TNG output from dump.

The output was incorrectly located in an if statement.
Partial fix of #1510

Change-Id: I85823d9369f208f21f4bafe19705e9e4dd2da027

History

#1 Updated by Erik Lindahl about 5 years ago

  • Target version changed from 5.0 to 5.x

#2 Updated by David van der Spoel about 5 years ago

Ok this one is not a show stopper, but #1502 is IMHO. Working on it now.

#3 Updated by David van der Spoel about 5 years ago

The example file in
gromacs/src/external/tng_io/example_files/tng_example.tng
can not be read by gromacs tng tools:

% gmx check -f gromacs/src/external/tng_io/example_files/tng_example.tng
Checking file gromacs/src/external/tng_io/example_files/tng_example.tng
Reading frame 0 time 0.000
  1. Atoms 15
    TNG library: Cannot read header size. /Users/spoel/GG/correl/gromacs/src/external/tng_io/src/lib/tng_io.c: 820
    TNG library: Cannot read block header at pos 2531. /Users/spoel/GG/correl/gromacs/src/external/tng_io/src/lib/tng_io.c: 18347

-------------------------------------------------------
Program gmx check, VERSION 5.1-dev-20140523-89c1dac-dirty
Source code file: gromacs/src/gromacs/fileio/tngio_for_tools.cpp, line: 743

File input/output error:
Cannot read TNG file. Cannot find data blocks of next frame.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

#4 Updated by David van der Spoel about 5 years ago

  • Subject changed from gmx dump does not work for tng files to gmx check and gmx dump do not work for tng files

#5 Updated by Gerrit Code Review Bot about 5 years ago

Gerrit received a related patchset '1' for Issue #1510.
Uploader: Magnus Lundborg ()
Change-Id: I85823d9369f208f21f4bafe19705e9e4dd2da027
Gerrit URL: https://gerrit.gromacs.org/3517

#6 Updated by Magnus Lundborg about 5 years ago

  • Status changed from New to Resolved

With these two associated revisions this should work now.

#7 Updated by Rossen Apostolov about 5 years ago

  • Status changed from Resolved to Closed

#8 Updated by Teemu Murtola about 5 years ago

  • Target version changed from 5.x to 5.0

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