# Issue: Unable to Remove PBC in GROMACS Using trjconv Options

**URL:** <https://gromacs.bioexcel.eu/t/issue-unable-to-remove-pbc-in-gromacs-using-trjconv-options/11780>\
**Category:** User discussions\
**Tags:** gmx-trjconv\
**Created:** [March 20, 2025, 7:13pm UTC](https://gromacs.bioexcel.eu/t/issue-unable-to-remove-pbc-in-gromacs-using-trjconv-options/11780 "2025-03-20T19:13:49Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![aguiarnetogm](https://avatars.discourse-cdn.com/v4/letter/a/58956e/32.png) [@aguiarnetogm](https://gromacs.bioexcel.eu/u/aguiarnetogm)\
**Post date:** [March 20, 2025, 7:13pm UTC](https://gromacs.bioexcel.eu/t/issue-unable-to-remove-pbc-in-gromacs-using-trjconv-options/11780/1 "2025-03-20T19:13:49Z")

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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.

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [March 24, 2025, 9:56am UTC](https://gromacs.bioexcel.eu/t/issue-unable-to-remove-pbc-in-gromacs-using-trjconv-options/11780/2 "2025-03-24T09:56:52Z")

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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

> **[Terminology - GROMACS 2025.1 documentation](https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow)**

Alessandra