Hi Mark, You are right. While I am writing,most of the things in my mind are lost :)
The actual command line is: g_cluster -s .tpr -f .xtc -dist and it gives a output file named rmsd-dist.xvg. In the first column, the rmsd values are written. However, I can not understand the values in the second column, the title of second column is only indicated. No explanation has been made in the manual. The frame number is 3000. One of the numbers on that column exceeds that value. -----Original Message----- From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Date: Fri, 15 Feb 2008 09:11:55 +1100 Subject: Re: [gmx-users] still got the problem with the output of g_cluster OZGE ENGIN wrote: > Hi all, > > I have still got the problem with the second column of the output of > g_cluster with -dist option. Xavier said that the a.u stands for arbitrary > unit and I think it gives the histogram of rmsd value distribution. If so, I > can not understand why the total of this column is not equal to the total > number of conformations obtained from the simulation. Well, what is it equal to? How many frames are you using, what are your actual command lines? Can you provide a short excerpt of the .xvg file? Please consider the point of view of the people of whom you're asking such a question. Unless they're actually fluent with the code and useage of g_cluster, they don't have the answer at their fingertips. However if you give them useful information, they might be able to see things that you can't. If you don't provide useful information, then even users who do have the answer at their fingertips might decide you're not worth their time :-) Mark _______________________________________________ gmx-users mailing list gmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin ================================= Computational Science & Engineering Koc University _______________________________________________ gmx-users mailing list gmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php