[gmx-users] Re: g_cluster

2013-07-09 Thread maggin
hi, Justin I read the paper Daura(1999) and other papers: "Ensemble-based convergence analysis of biomolecular trajectories"(2006) "Helix propensities of short peptide: Molecular dynamics versus bioinformatics" (2003) "Assessing equilibration and convergence in biomolecular simulation" (2002) bu

[gmx-users] Re: g_cluster segmentation fault

2011-03-29 Thread Craig Kitchen
Hi Mark, Works perfectly... Thanks, Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK On 26/03/11, Craig Kitchen wrote: Dear All, When running g_cluster on a file generated with g_mdmat I receive a segmentation fault. I have tried dif

Re: [gmx-users] Re: g_cluster settings

2010-07-12 Thread Ran Friedman
Marc - Note that you used the linkage method which maps a structure to a cluster if its distance to any structure already in the cluster is is less than the cutoff. If you think it's not representative of your system try another clustering method, but note that you may need a longer trajectory as w

[gmx-users] Re: g_cluster settings

2010-07-11 Thread Vitaly Chaban
Dear Marc: Please look towards g_clustzise (instead of g_cluster). We tried to use g_cluster some years ago and eventually switched to g_clustzise - I do not remember why but the latter was more successful. If you want to monitor the number of clusters in the system, g_clustzise can certainly do i