[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: 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
> with largest number of neighbors with all its neighbors as cluster and
> eliminate it from the pool of clusters. Repeat for remaining structures in
> 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 ?
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
João M. Damas
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
More information about the gromacs.org_gmx-users