Thank you very much Mark, it is clear to me now! -----Original Message----- From: [EMAIL PROTECTED] To: Discussion list for GROMACS users <[email protected]> Date: Fri, 15 Feb 2008 18:44:51 +1100 Subject: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster
So we're expecting a histogram of an all-against-all RMSD calculation over 3000-odd elements. So we should expect that around 3000*3000*0.5 entries exist in the histogram... that's about 4500000 entries. That sounds familiar, now :-) For 3002 elements, excluding self-comparisons, there are 3001-choose-2 combinations, i.e. 3001*3000*0.5, which is the number you give below. The values in this column are consistent with a histogram. Mark ----- Original Message ----- From: OZGE ENGIN <[EMAIL PROTECTED]> Date: Friday, February 15, 2008 6:32 pm Subject: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster To: [email protected] Cc: [email protected] > Sorry Mark, the sum of the 2 nd column is 4501500. The frame > number is 3002. > > > -----Original Message----- > From: [EMAIL PROTECTED] > To: Discussion list for GROMACS users <[email protected]> > Date: Fri, 15 Feb 2008 10:04:45 +1100 > Subject: Re: Re: [gmx-users] still got the problem with the > output of g_cluster > > What's the sum of the second column? > > Mark > > ----- Original Message ----- > From: OZGE ENGIN <[EMAIL PROTECTED]> > Date: Friday, February 15, 2008 9:46 am > Subject: Re: Re: [gmx-users] still got the problem with the > output of g_cluster > To: [email protected] > > > 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 <[email protected]> > > 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 [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 > > > > > > 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 > > > _______________________________________________ > 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 > > > 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 > _______________________________________________ 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 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
