[gmx-users] g_rdf (lyzozyme tutorial)

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 12 13:15:00 CEST 2012

On 6/12/12 5:16 AM, delara aghaie wrote:
> Dear Gromacs users
> Today I encountered a new error.
> I want to calculte RDF for my protein's (alpha-c) dissolved in water.
> when I use the command line:
> g_rdf -f traj.xtc -s topol.tpr -o rdf.xvg
> and I choose 3 for (C-alpha) for both the reference and target groups, every
> thing goes well and I will have the rdf plot.
> Now if I add option (-xy) to use the only x and y components, and then I choose
> my two groups, the program does not do anything and it stops !!
> This is right even for the lyzozyme protein in Justin's tutorial.

What version of Gromacs is this?  Does g_rdf simply stop, or does it produce an 
error?  Does it produce a segmentation fault?

Also note that the -xy option is much more useful for systems involving surfaces 
or membranes; I doubt it will be very informative for a system that tumbles in 3 
dimensions.  Notwithstanding, if there's a bug it should be fixed, but it may 
not be critical.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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