check | checkoverlap | checkstructure
Check for bad atomic overlaps or bond lengths. Can be used to skip corrupted frames.
check [<mask>] [around <mask2>] [reportfile <report>] [noimage] [skipbadframes] [offset <offset>] [cut <cut>] [nobondcheck] [silent]
[<mask>] Check structure of atoms in <mask> (all if not specified).
[around <mask2>] If specified, only check for problems between atoms in <mask> and atoms in <mask2>.
[reportfile <report>] Write any problems found to <report> (STDOUT if not specified).
[noimage] Do not image distances.
[skipbadframes] If errors are encountered for a frame, subsequent actions/trajectory output will be skipped.
[offset <offset>] Report bond lengths greater than the equilibrium value plus <offset> (default 1.0 Å)
[cut <cut>] Report atoms closer than <cut> (default 0.8 Å).
[nobondcheck] Check overlaps only.
[silent] Do not print information for bad frames – useful in conjunction with the skipbadframes option.
Check the structure and report problems related to atomic overlap/unusual bond length. Problems are reported when any two atoms in the mask are closer than <cut>. If bonds are being checked then bond lengths greater than their equilibrium value + <offset> are reported as well. This command can also be used to skip corrupted frames in a trajectory during processing. For example, if this message is encountered:
Warning: Frame 10 coords 1 & 2 overlap at origin; may be corrupt.
One could use check so that e.g. a subsequent distance command is not processed for bad frames:
check @1,2 skipbadframes silent distance d1 :1 :10
Usually frame corruption can be detected using only a few atoms, but this may not catch all types of corruption. The more atoms that are used the better the corruption detection will be, but the slower it will be to process the command. Typically a good procedure to follow when corruption is suspected is to run check using all important atoms (e.g. all solute heavy atoms) with the skipbadframes keyword followed by a trajout command to write all non-corrupt frames, for example:
trajin corrupted.crd check :1-13 skipbadframes silent trajout fixed.corrupted.nc