[gmx-developers] Clusterizing a long-time trajectories

[David van der Spoel]

Den 2018-07-26 kl. 14:02, skrev Boris Timofeev:
> Dear developers!
> 
> The existing realization of "gmx cluster" for calculations uses 
> RMSD-matrix,
> quadratically increasing with increase in length of a trajectory,
> and already since 20000 frames calculation of clusters becomes impossible
> because of requirements to memory and time.
> 
> Whether there are some special methods for a clustering of trajectories 
> of big duration,
> containing 100000 and more frames?
Use the -dr flag.
> 
> Best wishes
> Boris Timofeev.
> 
> 
> 
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se