[gmx-developers] [gmxana] gmx cluster is very buggy
David van der Spoel
spoel at xray.bmc.uu.se
Fri May 13 08:02:22 CEST 2016
On 13/05/16 05:38, Yunlong Liu wrote:
> Hi Gromacs developers,
> I recently used gmx cluster for cluster analysis but I got some very
> buggy result. The RMSD distribution I got is from 0.01 - 0.5 and I set a
> cutoff of 0.1. Why did the program give me only one cluster? When I
> remove the cutoff tag, (I thought the default value is 0.1 as well),
> then it gave me 30+ clusters.
If you suspect a bug please file a bug report on redmine.gromacs.org
> Also, I found "-om" tag and "-dm" tag is almost useless.
> *** A developer call ***
> As the trajectories getting larger and larger, a single core analysis
> program is more and more slow. For some analysis program, like "cluster
> analysis", they have such intrinsic properties that naturally support
> parallelism. Why not parallelize them to increase speed?
Lack of time...
> *Yunlong Liu / PhD Candidate*
> Email : davislong198833 at gmail.com
> Mario Amzel Lab, Biophysics Dept
> School of Medicine, JHU
> Address: 725 N Wolfe St, WBSB 601
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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