Bug #1194
Dihedral restraints in 4.5.X vs 4.6
Description
This is about starting simulation from a 4.5.5 tpr-file using 4.6 (or 4.6.1) that contains dihedral restraints.
I have made a small test-system with a dialanine-peptide in vacuum to reproduce the issue.
The system contains one single dihedral restraint (with arbitrary but reasonable values of phi, dphi, etc...)
System was prepared like this:
$grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr
Checking that it is there:
$gmxdump -s md.tpr |grep DIHRE Reading file md.tpr, VERSION 4.5.5 (single precision) functype[166]=DIHRES, label=0, power= 1 phi= 1.20000000e+02, dphi= 3.00000000e+01, kfac= 1.00000000e+00)
Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives me an error.
$ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md Reading file md.tpr, VERSION 4.5.5 (single precision) ------------------------------------------------------- Program mdrun, VERSION 4.6.1 Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136 Fatal error: symtab get_symtab_handle 1051260126 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------
Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works.
Thanks
Associated revisions
History
#1 Updated by Mark Abraham almost 6 years ago
- Description updated (diff)
- Affected version set to 4.6.1
#2 Updated by David van der Spoel almost 6 years ago
Posted fix in https://gerrit.gromacs.org/#/c/2353/
#3 Updated by Mark Abraham almost 6 years ago
- Status changed from New to Fix uploaded
#4 Updated by David van der Spoel over 5 years ago
- Status changed from Fix uploaded to Resolved
- % Done changed from 0 to 100
Applied in changeset 3ec882b8ec644943b15455e5e803a3a009cd686d.
#5 Updated by Mark Abraham over 5 years ago
- Status changed from Resolved to Closed
Fixes #1194 error reading 4.5.5 tpr files with dihres
Somehow the tpx_version produced by 4.5.5 was higher (73)
than expected, making the the tpx reading incorrectly
assuming this was using the new file format.
Now set to the version before the
first official 4.6 tpx format, 82 to match the tpr files
in the regression tests. Duh!
Change-Id: I40d8ffa0d350cf3b690f8dfb071fc191f027d02f