[gmx-users] number of clusters over time

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 28 06:39:57 CET 2014

On 2014-11-28 05:51, Steven Neumann wrote:
> Dear Users,
> Would anyone suggest which option of g_cluster provides the number of
> clusters gained over the simulation time? It would be an increasing plot
> reaching plateau when the simulation is converged.
> Please advise,
> Steven
How about running it multiple times with different -e time options?
You would have to postprocess to test whether the clusters from say the 
1st half of the simulation are the same as from the last half. Not 
entirely trivial, but if you find they are the same that is an 
indication your simulation has reached some sort of equilibrium.

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

More information about the gromacs.org_gmx-users mailing list