Bug #2081
trjconv should respect "-pbc whole" when another flag "-sep" is used
Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
simple
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
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