[gmx-users] g_rms

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 3 09:18:04 CEST 2007

andrea carotti wrote:
> Hi and thanks for answering to my previous question.
> Now I'm calculating the rmsd between two trajectories (-f2 option).
> One is made by 2200 frames and the other has 33 frames..Now I've some
> doubt about the output (rmsd.xvg), cause this file has only two columns
> with 2200 rows ...i was imaging that it should have 2200 rows and 33
> columns, am I wrong? 

You should be getting such a 2200x33 matrix. My guess is that the 
command line or files that you're using are not what you think they are :-)

> The second question is something that is already been asked before..it
> could be usefull to obtain the matrix 2200 x 33 in a human readable
> file. Is it possible without hacking the code? Perhaps using external
> scripts? 

There's a human readable matrix form that can already be written. Check 
out g_rms -h


More information about the gromacs.org_gmx-users mailing list