[gmx-users] Question about g_cluster
I recently started using g_cluster and have a question. When I run g_cluster, the program asks me to select two groups. The output looks something like this: Select group for least squares fit and RMSD calculation: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 0 Select group for output: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 1 I have assumed that g_cluster aligns the trajectory by the first group selected, and then clusters based on the second group. Recently, however, someone told me that both the alignment and the clustering is performed only on the first group. Can anyone confirm this? If so, what's the purpose of the second group? Thanks, Jacob ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Question about g_cluster
Jacob Durrant wrote: I recently started using g_cluster and have a question. When I run g_cluster, the program asks me to select two groups. The output looks something like this: Select group for least squares fit and RMSD calculation: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 0 Select group for output: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 1 I have assumed that g_cluster aligns the trajectory by the first group selected, and then clusters based on the second group. Recently, however, someone told me that both the alignment and the clustering is performed only on the first group. Can anyone confirm this? If so, what's the purpose of the second group? I agree that output is ambiguous. g_cluster -h is also silent on both the need to provide these groups and what they're used for. Perhaps an improvement to the documentation is in order. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] Question about g_cluster groups
Hi all, I'm using g_cluster with the -dm option to provide a pre-calculated RMSD-matrix of my trajectory. I therefore assume than g_cluster won't need to do any RMSD calculations, since it can take all the distance information it needs from the xpm matrix. Nevertheless g_cluster asks me to provide a group for LSQ fitting and one for RMSD calculation. Why? Thank you. -==_///_/-=-_/-=-_-==_//-//--/- Marco Pasi, PhD Student Department of Biotechnology and Biosciences University of Milan-Bicocca Piazza della Scienza, 2 20126 Milan - Italy Phone: +39.02.64483475 E-mail: [EMAIL PROTECTED] -=_///-=--_//=---=_/---///-==///-- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
