gmx clustsize -mol ignores index file
When running gmx clustsize -mol the index file is ignored, meaning all water is taken into account as well when doing the analysis on a bunch of solute molecules.
Problem be circumvented by making a subset of the trajectory first.
#3 Updated by Erik Lindahl about 3 years ago
- Status changed from Accepted to Rejected
The output of gmx clustsize clearly states "Using molecules rather than atoms. Not reading index file" in this case, so this is not a bug but rather functionality that was never implemented.
The only way for a generic tool to automatically handle the combination of indices and molecule-based properties would be for the tool to first check that the index file corresponds to only molecules, and then go through the entire topology to create a subset consisting of only the molecules you are interested in.