Re: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster
Thank you very much Mark, it is clear to me now! -Original Message- From: [EMAIL PROTECTED] To: Discussion list for GROMACS users 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 450 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: gmx-users@gromacs.org Cc: gmx-users@gromacs.org > 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 > 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: gmx-users@gromacs.org > > > 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 > > 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 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > Ozge Engin > > = > > Computational Science & Engineering > > Koc University > > ___ > > 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 interfac
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 450 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: gmx-users@gromacs.org Cc: gmx-users@gromacs.org > 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 > 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: gmx-users@gromacs.org > > > 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 > > 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 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > Ozge Engin > > = > > Computational Science & Engineering > > Koc University > > ___ > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/li
Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster
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 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: gmx-users@gromacs.org > 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 > 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 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > Ozge Engin > = > Computational Science & Engineering > Koc University > ___ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science & Engineering Koc University ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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: gmx-users@gromacs.org > 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 > 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 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > Ozge Engin > = > Computational Science & Engineering > Koc University > ___ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] still got the problem with the output of g_cluster
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 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 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science & Engineering Koc University ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
