# How to extract middle cluster structure form gmx\_cluster output file cluster.pdb

**URL:** <https://gromacs.bioexcel.eu/t/how-to-extract-middle-cluster-structure-form-gmx-cluster-output-file-cluster-pdb/13425>\
**Category:** User discussions\
**Created:** [April 29, 2026, 6:03am UTC](https://gromacs.bioexcel.eu/t/how-to-extract-middle-cluster-structure-form-gmx-cluster-output-file-cluster-pdb/13425 "2026-04-29T06:03:47Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Nainsybaghel](https://avatars.discourse-cdn.com/v4/letter/n/9fc29f/32.png) [@Nainsybaghel](https://gromacs.bioexcel.eu/u/Nainsybaghel)\
**Post date:** [April 29, 2026, 6:03am UTC](https://gromacs.bioexcel.eu/t/how-to-extract-middle-cluster-structure-form-gmx-cluster-output-file-cluster-pdb/13425/1 "2026-04-29T06:03:47Z")

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Hi…

I used gmx clustering command line, which generated clusters.pdb file. When I opened the file in PyMOL, it had cluster 1 with 70 structures and cluster 2 with 1. As I understand it, cluster 1 contains all selected frames, and cluster 2 contains the middle structure, and we should consider cluster 2 for further analysis. **Please give me some clarification regarding this**.

Also, cluster.pdb file is very large to open, it’s approximately 5170469 KB. That’s why I want to extract only the middle cluster image from cluster.pdb. which will be easy to handle. **Please provide some suggestions to implement this approach**.

Here is the command that I used:

gmx cluster -s md\_0\_1.tpr -f md1.xtc -cutoff 0.30 -method gromos -g -cl

Here is the file opened in PyMOL.

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1d7f8879341bfe494f319a439c7fd62d81c6b421.jpeg)

give me your valuable suggestions.

Thankyou.