Hi all, I would really appreciate if someone can help me with the "group for output" option on g_cluster.
When I use g_cluster, it asks me to select two groups. A gourd for fit and RMSD calculation and a group for output: Select group for least squares fit and RMSD calculation: Group 0 ( System) has 205722 elements Group 1 ( Protein) has 10337 elements Group 2 ( Protein-H) has 8036 elements Group 3 ( C-alpha) has 1005 elements Select group for output: Group 0 ( System) has 205722 elements Group 1 ( Protein) has 10337 elements Group 2 ( Protein-H) has 8036 elements Group 3 ( C-alpha) has 1005 elements Know, I have always assumed that g_cluster do a fit and calculate the RMSD matrix based on the trajectory of the first group, and the second group is just for control what atoms will be written to the output file. Recently, however, I did some tests and it seems that the different groups chosen for "output group" effect not only the atoms written to the output file, but also the clustering results. Can anyone confirm this? Cheers, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au ============================================ the second group? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
