[gmx-users] Reference of the algorithm gromos in g_cluster

João M. Damas jmdamas at itqb.unl.pt
Fri May 1 15:41:36 CEST 2015

It's on the second paragraph of the "Experimental Section". The entire

Note: the middle of cluster from g_cluster is not the same as the method's
center of cluster.


On Fri, May 1, 2015 at 8:27 AM, Antonio De Nicola <adenicola at unisa.it>

> I used the tool g_cluster of gromacs (4.5.1) to obtain clusters from my
> simulations. As option of g_cluster, you can chose the cluster algorithm
> gromos.
> "gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed.
> 1999, 38, pp 236-240). Count number of neighbors using cut-off, take
> structure
> with largest number of neighbors with all its neighbors as cluster and
> eliminate it from the pool of clusters. Repeat for remaining structures in
> pool."
> The reference of Daura seems not correct. In such paper  I did not found
> information or description about how the algorithm works.
> Someone has a correct reference or can help me to find it ?
> best,
> Antonio
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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