rerun function returns fault error on trajectory which passed gmx check
I tried to run mdrun rerun on a trajectory which has been generated previously, using gmx mdrun -deffnm prod -rerun prod.trr.
And I have encountered:
Number of atoms in trajectory (-1) does not match the run input file (91497)
gmx check -f prod.trr
Checking file prod.trr
trr version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
- Atoms 91497
Last frame 2 time 4.000
Item #frames Timestep (ps)
Step 3 2
Time 3 2
Lambda 3 2
Coords 3 2
Box 3 2
The trajectory can be reproduced by running prod.tpr which is a 5ps simulation.
gmx mdrun -deffnm prod
#1 Updated by Mark Abraham 6 months ago
- Category set to mdrun
- Status changed from New to Accepted
- Priority changed from High to Low
- Target version set to 2018.4
Thanks for the report.
gmx mdrun -deffnm prod -rerun prod.trr causes the output trajectory to be named prod.trr, which is apparently interfering with reading the rerun file of the same name.
gmx mdrun -s prod -rerun prod.trr works, and is how I suggest Zhiyi proceeds.
mdrun should refuse to start the rerun if either trajectory output filename matches the rerun input filename.