How do I correctly re-wrap DCLE tail-solvent and lipids in an HMMM trajectory?

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GROMACS version: 2023.3
GROMACS modification: No

Screenshot from 2025-08-07 08-59-27
Screenshot from 2025-08-07 08-59-27593×348 113 KB

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The system contains:

  • 3 single-pass membrane protein (∼3 k atoms)

  • 400 truncated POPC lipids

  • 2 000 DCLE tail-solvent molecules

  • TIP3P water + 0.15 M NaCl

what i did so far:gmx_mpi trjconv -s step7_1.tpr -f 200ns.xtc -pbc mol -center -o center.xtc -n index.ndx

Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Select group for centering
Group 0 ( SOLU) has 19071 elements
Group 1 ( MEMB) has 91324 elements
Group 2 ( SOLV) has 323925 elements
Group 3 ( SOLU_MEMB) has 110395 elements
Group 4 ( SYSTEM) has 434320 elements
Select a group: 1
Selected 1: ‘MEMB’
Select group for output
Group 0 ( SOLU) has 19071 elements
Group 1 ( MEMB) has 91324 elements
Group 2 ( SOLV) has 323925 elements
Group 3 ( SOLU_MEMB) has 110395 elements
Group 4 ( SYSTEM) has 434320 elements
Select a group: 3
Selected 3: ‘SOLU_MEMB’
Reading frame 0 time 0.000
Precision of 200ns.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Back Off! I just backed up center.xtc to ./#center.xtc.1#
Last frame 2000 time 200000.000 → frame 1999 time 199900.000
→ frame 2000 time 200000.000
Last written: frame 2000 time 200000.000

then: gmx_mpi trjconv -s step7_1.tpr -f center.xtc -pbc whole -o whole.xtc -n index.ndx
:-) GROMACS - gmx trjconv, 2023.5-plumed_2.11.0_dev (-:

Executable: /usr/local/gromacs/bin/gmx_mpi
Data prefix: /usr/local/gromacs
Working dir: /home/nadia/smit/anm/w.omlac
Command line:
gmx_mpi trjconv -s step7_1.tpr -f center.xtc -pbc whole -o whole.xtc -n index.ndx

Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Reading file step7_1.tpr, VERSION 2023.3 (single precision)
Select group for output
Group 0 ( SOLU) has 19071 elements
Group 1 ( MEMB) has 91324 elements
Group 2 ( SOLV) has 323925 elements
Group 3 ( SOLU_MEMB) has 110395 elements
Group 4 ( SYSTEM) has 434320 elements
Select a group: 3
Selected 3: ‘SOLU_MEMB’
Reading frame 0 time 0.000
Precision of center.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Back Off! I just backed up whole.xtc to ./#whole.xtc.1#
Last frame 2000 time 200000.000 → frame 1999 time 199900.000
→ frame 2000 time 200000.000
Last written: frame 2000 time 200000.000
After step 2 the bilayer looks disintegrated: lipids are in pieces and DCLE clouds appear far above/below the slab (screenshot attached). Skipping -pbc nojump keeps the bilayer intact, but then individual DCLE molecules jump across the box edges frame-to-frame.

What I’m looking for

  1. A robust command sequence (or FixBox settings) that

    • keeps each POPE lipid and each DCLE molecule whole,

    • centers the protein/bilayer in Z,

    • gives a continuous trajectory suitable for APL, RMSD, etc.