[gmx-users] still got the problem with the output of g_cluster

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 14 23:11:55 CET 2008

> 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 :-)


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