Issue: Unable to Remove PBC in GROMACS Using trjconv Options

User discussions
1

GROMACS version: 2021.3
GROMACS modification: No

Hello everyone,

I’m trying to remove periodic boundary conditions (PBC) from my trajectory using gmx trjconv, but none of the options I’ve tried seem to work correctly. I have tested different -pbc and -fit options, but my system still appears fragmented or incorrectly wrapped.

What I Have Tried

1. Using -pbc Options:

I tested the following:

  • -pbc mol: Keeps molecules whole but does not remove PBC effects.
  • -pbc whole: Does not prevent molecules from jumping across boundaries.
  • -pbc nojump: Still results in broken molecules.
  • -pbc cluster: Groups molecules together, but some atoms still appear outside the main cluster.

2. Using -fit Options:

  • -fit rot+trans: Did not correctly align the system after removing PBC.
  • -fit translation: Did not seem to make a difference.

3. Combining -pbc with -center and -ur:

  • -center with -boxcenter rect or tric: The system appears centered but still fragmented.
  • -ur compact: Does not seem to change the outcome.

Expected Outcome

I need a trajectory where all molecules remain whole, properly aligned, and centered inside the simulation box without PBC artifacts.

2

HI,
Fixing periodicity effects with gmx trjconv may need multiple invocations and the order of the command matter.
Please have a look at this workflow that may help you to solve the problem and understand the order of the invocations

Alessandra