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Bug #2081

trjconv should respect "-pbc whole" when another flag "-sep" is used

Added by Mateusz Bieniek over 4 years ago. Updated about 3 years ago.

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

The trjconv command currently does not make the molecules whole while outputting several pdbs at the same time.

The command I used is:
gmx trjconv -s nvt1.tpr -f nvt1.xtc -sep -pbc whole -o frame.pdb -n whole_butGold


Related issues

Related to GROMACS - Task #2115: trjconv does too many things, and combinations of them work poorlyNew

History

#1 Updated by Mark Abraham over 4 years ago

Thanks for the report. Yes, trjconv is not designed well enough for all of its options to work in intuitive ways when combined. We need to re-write the tool in separate modules that can then be combined to work well. I will see if there's a simple fix for this, however.

#2 Updated by Mark Abraham about 4 years ago

  • Related to Task #2115: trjconv does too many things, and combinations of them work poorly added

#3 Updated by Erik Lindahl about 3 years ago

  • Status changed from New to Rejected

Tested with release-2018 without problems for a small water box - the molecules are made whole with "pbc mol". Please reopen and upload specific example files if this is still present in the latest release.

#4 Updated by Erik Lindahl about 3 years ago

  • Status changed from Rejected to Closed

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