Thank you Mark for your feedbacks. There is one more point that is not clear to me for the output of g_cluster, In the second column of the "cluster.log" of g_cluster, the same rmsd values are indicated for different clusters. What does it mean? Although these clusters have the same cut-off value, they are grouped in different clusters, Why?
Thank you. -----Original Message----- From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Date: Sun, 17 Feb 2008 22:35:20 +1100 Subject: Re: [gmx-users] distance options for g_cluster OZGE ENGIN wrote: > Hi all, > > I am trying to understand what type of distance can be used with g_cluster? > > In the manual, it is written that RMS deviation after fitting or RMS > deviation of atom-pair distances can be used to define the distance between > structures in the first paragraph. > However, in the "other options" part, two options are indicated for > -dista option, which indicates the type of distance that will be used with > g_cluster. They are RMSD of distances or RMS deviation. Consequently, the > information in the "first paragraph" does not coincide with that given in the > "other options" part for -dista option. > > Maybe I could not understand. Could anyone explain this in a clearer way, > please? I agree that it is not very clear what is meant in the documentation, and I have wondered myself what it means. This is one of the reasons that the source code is made available. I had a quick look, and "-dista yes" looks like it implements the "RMS deviation of atom-pair distances" quoted above. That is, it forms an atom-pair distance matrix for each structure in the trajectory, and then does an all-against-all root-mean-square comparison of those matrices to generate the structure comparison matrix for clustering. You'd be well advised to verify that yourself. It's all in src/tools/gmx_cluster.c Mark _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php is made available. I had a quick look, and "-dista yes" looks like it implements the "RMS deviation of atom-pair distances" quoted above. That is, it forms an atom-pair distance matrix for each structure in the trajectory, and then does an all-against-all root-mean-square comparison of those Ozge Engin ================================= Computational Science & Engineering Koc University _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
