Re: [gmx-users] clustering and representative structure

, through a comparison of the central structures from different methods. A very good reference on clustering is the book by J.A. Hartigan Clustering Algorithms. Best regards, Nikos Sgourakis Carlos Javier Nuñez Aguero wrote: Hi all, How are you? In Gromacs, the clustering methods are: o Full

Re: [gmx-users] REMD demuxing

Hello, Instead of using system calls, you may also use the pymacs python interface by Daniel Seelinger: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/dseelig/pymacs.html You can access all information in an xtc file in an object-oriented manner. Nikos Andrea C. Vaiana wrote: Hello

[gmx-users] k-means clustering in GROMACS

Dear GROMACS users, Here I have implemented the k-means clustering algorithm in the original GROMACS module, gmx_cluster.c (called by the wrapper g_cluster). k-means is a heuristic algorithm that finds the partition of n points (conformations) in k groups (clusters), such that the sum of the

[gmx-users] g_cluster -dm

Hello, I am trying to use g_cluster. However, the result I am obtaining when using a pre-calculated RMSD matrix with the -dm option is quite different than the one I get when the RMSD matrix is calculated by g_cluster from a trjectory of structures. Is this a matter of precision in the xpm