VMD-L Mailing List

From: Zuzanna Jedlinska (zuzannaj_at_sas.upenn.edu)
Date: Fri Jul 07 2023 - 08:54:50 CDT

Hi,

I am having issues using CatDCD 5.2 (and also version 5.1) to convert from
lammpstrj file to dcd.
I have periodic boundary conditions in all directions.
The error seems to be the expected number of atoms vs the number in the
actual file.

2D case:

./catdcd -o out2d.dcd -lammpstrj traj2D.lammpstrj

Output:

CatDCD 5.2
Opening file 'out2d.dcd' for writing.
Opened file 'traj2D.lammpstrj' for reading.
lammpsplugin) New style dump with 5 data fields. Coordinate data flags: 0x02
lammpsplugin) Reconstructing atomic coordinates from fractional coordinates
and box vectors.
lammpsplugin) Too many atoms in timestep. 8141 vs. 0
Read 0 frames from file traj2D.lammpstrj, wrote 0.
Total frames: 0
Frames written: 0
CatDCD exited normally

-----------------------------------

3D case:

 ./catdcd -o out3d.dcd -lammpstrj traj3D.lammpstrj

Output:

CatDCD 5.2
Opening file 'out3d.dcd' for writing.
Opened file 'traj3D.lammpstrj' for reading.
lammpsplugin) New style dump with 7 data fields. Coordinate data flags: 0x01
lammpsplugin) Using absolute atomic coordinates directly.
lammpsplugin) Too many atoms in timestep. 48000 vs. 16
Read 0 frames from file traj3D.lammpstrj, wrote 0.

Kindly,
Zuzanna