[gmx-developers] [gmxana] gmx cluster is very buggy

[David van der Spoel]

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...

>
> Best
> Yunlong
>
>
>
> --
>
> ==================================
> *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