Gmx clustsize - clusters in the gas phase

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GROMACS version:ubuntu 2023.2
GROMACS modification: No
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From the definition - gmx clustsize computes the size distributions of molecular/atomic clusters in the gas phase, so if you have a molecule forming aggregates in solution not in the gas phase, what do you do?

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There may be better options but here are my ideas for protein aggregation:

  1. Radial Distribution Function (RDF): Calculate RDF between protein centers of mass to understand protein-protein interactions. Sudden peaks in RDF can indicate aggregation.
  2. Clustering Analysis: Utilize clustering algorithms (like GROMACS’ gmx cluster or other clustering methods) to identify protein clusters in the simulation box. This helps in quantifying the extent of aggregation.
  3. SASA (Solvent Accessible Surface Area): Monitor changes in SASA over time. Aggregating proteins may exhibit reduced SASA due to buried surface areas.
  4. Hydrogen Bond Analysis: Analyze hydrogen bonding patterns between proteins to identify regions of interaction and potential aggregation interfaces.
  5. Principal Component Analysis (PCA): Perform PCA to study collective motions of proteins. Aggregates might show distinct correlated movements.
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Hi, Thanks for the suggestions. The issue is that gmx clustsize actually works for atoms, the manual pages say if you put -mol as option it will work for molecules, but it doesn’t. The program just hangs. It seems to be a bug.