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Bug #1194

Dihedral restraints in 4.5.X vs 4.6

Added by Per Larsson over 4 years ago. Updated about 4 years ago.

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

diala.pdb - Pdb file with input coordinates (1.59 KB) Per Larsson, 03/18/2013 03:21 PM

topol.top - charmm36 topology with dihedral restraint in an #ifdef (7.05 KB) Per Larsson, 03/18/2013 03:21 PM

conf.gro - processed coordinates (1.1 KB) Per Larsson, 03/18/2013 03:21 PM

md.mdp - mdp-file (10.2 KB) Per Larsson, 03/18/2013 03:21 PM

md.tpr - tpr file with restraint (66.3 KB) Per Larsson, 03/18/2013 03:21 PM

Associated revisions

Revision 3ec882b8 (diff)
Added by David van der Spoel about 4 years ago

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

History

#1 Updated by Mark Abraham over 4 years ago

  • Description updated (diff)
  • Affected version set to 4.6.1

#3 Updated by Mark Abraham about 4 years ago

  • Status changed from New to Fix uploaded

#4 Updated by David van der Spoel about 4 years ago

  • Status changed from Fix uploaded to Resolved
  • % Done changed from 0 to 100

#5 Updated by Mark Abraham about 4 years ago

  • Status changed from Resolved to Closed

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