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Bug #1775

Grompp checkpoint error

Added by Dries Van Rompaey over 2 years ago. Updated over 1 year ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Hi everyone,

I’m experiencing some discrepancies when I pass the checkpoint file to
grompp using the -t checkpoint flag:

grompp -f md.mdp -o md.tpr -p topol.top -c md_res_1000.gro -t md_res_1000.cpt

This command results in a tpr file without any variables for barostat and
thermostat. These values are, however, present in the cpt file.

Running the tpr file and additionally providing the checkpoint through the
‘mdrun -cpi’ command produces a different output than running mdrun using
the same tpr (even though the checkpoint has already been passed into
grompp).

Kind regards

Dries

md_res_1000.cpt (565 KB) md_res_1000.cpt input checkpoint file Dries Van Rompaey, 07/13/2015 08:37 AM
md_res_1000.gro (1.58 MB) md_res_1000.gro input gro file Dries Van Rompaey, 07/13/2015 08:37 AM
posre.itp (30.6 KB) posre.itp input positional restraints Dries Van Rompaey, 07/13/2015 08:37 AM
topol.top (554 KB) topol.top input topology Dries Van Rompaey, 07/13/2015 08:37 AM
md.tpr (1.1 MB) md.tpr tpr generated by grompp Dries Van Rompaey, 07/13/2015 08:37 AM
md.mdp (1.98 KB) md.mdp input mdp file Dries Van Rompaey, 07/13/2015 08:38 AM

Associated revisions

Revision 9457e6db (diff)
Added by Mark Abraham about 2 years ago

Update advice about grompp -t

grompp -t state.cpt does not copy coupling-algorithm state from a .cpt
into the new .tpr, even though it can still do so from grompp -e.

Refs #1775

Change-Id: I8c4d68fc8d3750b79f30c0f77115c80e1f3cf9b3

History

#1 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #1775.
Uploader: Mark Abraham ()
Change-Id: I8c4d68fc8d3750b79f30c0f77115c80e1f3cf9b3
Gerrit URL: https://gerrit.gromacs.org/4892

#2 Updated by Mark Abraham over 2 years ago

Thanks for the report. I've amended the docs to make clear how the subsequent restart should be run.

In principle this could be made to work - old-style gmx grompp -t traj.trr -e ener.edr still seems to have code, so code could be written to get the information from gmx grompp -t state.cpt. However, the future of ensemble-preserving restarts will be all about the checkpoint file, and we need to reduce the number of code paths we maintain, so I will probably plan to remove some/all of gmx grompp -t -e (in master branch sometime).

#3 Updated by Erik Lindahl over 1 year ago

  • Status changed from New to Resolved

Resolved, for certain values of "resolved".

#4 Updated by Erik Lindahl over 1 year ago

  • Status changed from Resolved to Closed

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