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

Yunlong Liu yliu120 at jh.edu
Fri May 13 07:38:58 CEST 2016

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.

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?



*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

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