# \#gmx-cluster

**URL:** https://gromacs.bioexcel.eu/tag/gmx-cluster/70.md

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## [Making a trajectory by listing frames](https://gromacs.bioexcel.eu/t/making-a-trajectory-by-listing-frames/12163)

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**Author:** [@Bridi](https://gromacs.bioexcel.eu/u/Bridi)\
**Replies:** 1\
**Last updated:** [May 28, 2025, 1:29pm UTC](https://gromacs.bioexcel.eu/t/making-a-trajectory-by-listing-frames/12163 "2025-05-28T13:29:19Z")

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GROMACS version: 2024.04 GROMACS modification: No I have a text file with more than ten thousand frames listed from clustering, which i need to make a new trajectory from a pre-existing original trajectory. I already t…

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## [Writing the full RMSD matrix in gmx cluster](https://gromacs.bioexcel.eu/t/writing-the-full-rmsd-matrix-in-gmx-cluster/10879)

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**Author:** [@ncheron](https://gromacs.bioexcel.eu/u/ncheron)\
**Replies:** 2\
**Last updated:** [January 10, 2025, 10:09pm UTC](https://gromacs.bioexcel.eu/t/writing-the-full-rmsd-matrix-in-gmx-cluster/10879 "2025-01-10T22:09:13Z")

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Dear developers, First, thanks a lot for all your efforts. I am writing to ask if it is possible to add a small feature to gmx cluster, which is the possibility to write the full RMSD matrix in a file that could be read…

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## [Using dynamic indices for outputting cluster centroids](https://gromacs.bioexcel.eu/t/using-dynamic-indices-for-outputting-cluster-centroids/10998)

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**Author:** [@fatpmeireles](https://gromacs.bioexcel.eu/u/fatpmeireles)\
**Replies:** 0\
**Last updated:** [January 10, 2025, 3:58pm UTC](https://gromacs.bioexcel.eu/t/using-dynamic-indices-for-outputting-cluster-centroids/10998 "2025-01-10T15:58:55Z")

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GROMACS version:2024.2 GROMACS modification: Yes/No Hi, I’m analyzing different conformations that a protein-ligand complex adopts by clustering my production trajectory. An important part of this complex is a structu…

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## [Clustering analysis - Gromacs](https://gromacs.bioexcel.eu/t/clustering-analysis-gromacs/8500)

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**Author:** [@nabilnour](https://gromacs.bioexcel.eu/u/nabilnour)\
**Replies:** 1\
**Last updated:** [March 5, 2024, 1:28am UTC](https://gromacs.bioexcel.eu/t/clustering-analysis-gromacs/8500 "2024-03-05T01:28:45Z")

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GROMACS version: 21.0 GROMACS modification: No Can you please provide me a step by step command lines to complete clustering analysis and Free energy landsacape using modules : gmx cluster module & gmx sham module ?

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## [Gmx clustsize - clusters in the gas phase](https://gromacs.bioexcel.eu/t/gmx-clustsize-clusters-in-the-gas-phase/7711)

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**Author:** [@reaham](https://gromacs.bioexcel.eu/u/reaham)\
**Replies:** 2\
**Last updated:** [November 27, 2023, 3:35pm UTC](https://gromacs.bioexcel.eu/t/gmx-clustsize-clusters-in-the-gas-phase/7711 "2023-11-27T15:35:27Z")

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GROMACS version:ubuntu 2023.2 GROMACS modification: No Here post your question From the definition - gmx clustsize computes the size distributions of molecular/atomic clusters in the gas phase, so if you have a molecu…