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Bug #1502

trjconv incorrect tng defaults

Added by David van der Spoel almost 3 years ago. Updated almost 3 years ago.

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

When converting a .trr file to .tng, only one in five coordinate frames are stored and no velocities, despite the default options being:
-[no]vel (yes) Read and write velocities if possible
-skip <int> (1) Only write every nr-th frame
-dt <time> (0) Only write frame when t MOD dt = first time (ps)

traj2.trr - Trajectory file to reproduce the problem. (704 KB) David van der Spoel, 05/15/2014 09:54 AM

topol.tpr - Topology needed to do the test. (120 KB) David van der Spoel, 05/22/2014 02:40 PM

Associated revisions

Revision 11e170d2 (diff)
Added by David van der Spoel almost 3 years ago

Permit trjconv to read and write velocities with TNG files

Partial fix of #1502

This set velocity reading and writing on for tng file in trjconv.
However there still is a problem with the number of frames being
reduced at each conversion.

Change-Id: I91e7f5245ca75ebb9dd8e4450f94015b5c3f2bfa

Revision 758eba66 (diff)
Added by Magnus Lundborg almost 3 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

History

#1 Updated by David van der Spoel almost 3 years ago

% gmx check -f traj2
<snip>
Item #frames Timestep (ps)
Step 6 0.004
Time 6 0.004
Lambda 6 0.004
Coords 6 0.004
Velocities 6 0.004
Forces 0
Box 6 0.004

% gmx check -f traj2.tng
<snip>

% gmx trjconv -f traj2.trr -o traj2.tng -vel
<snip>
Item #frames Timestep (ps)
Step 2 0.02
Time 2 0.02
Lambda 2 0.02
Coords 2 0.02
Velocities 0
Forces 0
Box 2 0.02

Adding the tpr file on the command line does not make a difference.

#2 Updated by Magnus Lundborg almost 3 years ago

Thanks for the report and the file to reproduce it. I will have a look at it as soon as possible.

#3 Updated by David van der Spoel almost 3 years ago

#4 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1502.
Uploader: David van der Spoel ()
Change-Id: I91e7f5245ca75ebb9dd8e4450f94015b5c3f2bfa
Gerrit URL: https://gerrit.gromacs.org/3500

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

  • Target version changed from 5.x to 5.0

#6 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1502.
Uploader: Magnus Lundborg ()
Change-Id: I5275382bd49b5b46ebfdebe535c53d2f09015bc0
Gerrit URL: https://gerrit.gromacs.org/3514

#7 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1502.
Uploader: David van der Spoel ()
Change-Id: I91e7f5245ca75ebb9dd8e4450f94015b5c3f2bfa
Gerrit URL: https://gerrit.gromacs.org/3523

#8 Updated by Magnus Lundborg almost 3 years ago

  • Status changed from New to Resolved
  • % Done changed from 0 to 100

#9 Updated by Rossen Apostolov almost 3 years ago

so can we close this one?

#10 Updated by Erik Lindahl almost 3 years ago

  • Status changed from Resolved to Closed

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