GROMACS version: 5.1.4
GROMACS modification: Yes/No
Dear all,
We have done cluster analysis through gmx cluster with cutoff 1.2 nm as our protein is showing up to 1.5 nm RMSD of backbone atoms using the method gromos but it shows the warning as follows:
WARNING: rmsd cutoff 1.5 is outside range of rmsd values 0.032871 to 0.906573
WARNING: rmsd minimum 0 is below lowest rmsd value 0.032871
Anybody can suggest me regarding these warnings and what cutoff should we use for this system.
Hi,
gmx cluster tool can use different methods/approaches to make cluster. I suggest to look up in literature the cluster approach (you plan to use) to see how the cut-off is defined and applied. That will help you to find the best values.
Best regards
Alessandra