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