Bug #741
tpbconv can not read cpt file
Description
tpbconv crashes with the following command line:
tpbconv -s topol.tpr -f state.cpt -until 220 -o cont.tpr
with the following error:
------------------------------
Program tpbconv, VERSION 4.5.3
Source code file: ../../../gromacs-4.5.3/src/kernel/tpbconv.c, line: 451
Fatal error:
Number of atoms in Topology (11000) is not the same as in Trajectory (0)
-----------------------------
However, gmxcheck does find the coordinates in the cpt file:
Coords 1
Velocities 1
Forces 0
Box 1
Since mdrun does not allow to specify the number of extra steps to be taken tpbconv should at least be able to get all information from the checkpoint file. The -maxh option of mdrun is not a good replacement in all cases.
Associated revisions
History
#1 Updated by Szilárd Páll about 8 years ago
- Target version deleted (
4.5.4)
#2 Updated by Rossen Apostolov about 8 years ago
Is this still an issue? Do we want it fixed for 4.5.5?
#4 Updated by Mark Abraham about 8 years ago
Note that this might still require mdrun -cpi for an ensemble-preserving restart.
grompp -t .cpt does require mdrun -cpi, because grompp does not preserve ekinstate, because the t_trxframe filled by read_first_frame() from the .cpt does not store ekinstate.
tpbconv -f .cpt looks like it is better because read_checkpoint_state() does read ekinstate, but the do_tpx() called by read_tpx_state() in runner() doesn't read ekinstate, even if the .tpr file format could/does contain ekinstate.
tpbconv can now read cpt files, fixes #741