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Bug #741

tpbconv can not read cpt file

Added by David van der Spoel over 8 years ago. Updated over 8 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
-
Affected version - extra info:
4.5.3
Affected version:
Difficulty:
uncategorized
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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

Revision ba15d988 (diff)
Added by Berk Hess over 8 years ago

tpbconv can now read cpt files, fixes #741

History

#1 Updated by Szilárd Páll over 8 years ago

  • Target version deleted (4.5.4)

#2 Updated by Rossen Apostolov over 8 years ago

Is this still an issue? Do we want it fixed for 4.5.5?

#3 Updated by Berk Hess over 8 years ago

  • Status changed from New to Closed

I fixed it.

#4 Updated by Mark Abraham over 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.

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