Bug #1502
trjconv incorrect tng defaults
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)
Associated revisions
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 about 5 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 about 5 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 about 5 years ago
#4 Updated by Gerrit Code Review Bot about 5 years ago
Gerrit received a related patchset '1' for Issue #1502.
Uploader: David van der Spoel (davidvanderspoel@gmail.com)
Change-Id: I91e7f5245ca75ebb9dd8e4450f94015b5c3f2bfa
Gerrit URL: https://gerrit.gromacs.org/3500
#5 Updated by David van der Spoel about 5 years ago
- Target version changed from 5.x to 5.0
#6 Updated by Gerrit Code Review Bot about 5 years ago
Gerrit received a related patchset '1' for Issue #1502.
Uploader: Magnus Lundborg (magnus.lundborg@scilifelab.se)
Change-Id: I5275382bd49b5b46ebfdebe535c53d2f09015bc0
Gerrit URL: https://gerrit.gromacs.org/3514
#7 Updated by Gerrit Code Review Bot about 5 years ago
Gerrit received a related patchset '1' for Issue #1502.
Uploader: David van der Spoel (davidvanderspoel@gmail.com)
Change-Id: I91e7f5245ca75ebb9dd8e4450f94015b5c3f2bfa
Gerrit URL: https://gerrit.gromacs.org/3523
#8 Updated by Magnus Lundborg about 5 years ago
- Status changed from New to Resolved
- % Done changed from 0 to 100
Applied in changeset 758eba66aab63ff5697f07db6d62d5b48e90a0a8.
#9 Updated by Rossen Apostolov about 5 years ago
so can we close this one?
#10 Updated by Erik Lindahl about 5 years ago
- Status changed from Resolved to Closed
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