[gmx-developers] Clusterizing a long-time trajectories

[Boris Timofeev]

Dear David!

Option  -dr, it is new?
Perhaps, you meant - dt? There is no wish to thin out a trajectory.
Sincerely,
Boris.
>Суббота,  4 августа 2018, 16:09 +03:00 от David van der Spoel <spoel at xray.bmc.uu.se>:
>
>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
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-- 
Boris Timofeev
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