[gmx-users] radial distribution function

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 9 21:37:50 CEST 2011

Moeed wrote:
> Dear users,
> I have created radial distribution function plot for Carbon atoms in a 
> system containing polymer chains. I see some little jumps between first 
> and second peak.
> I need your help to comment on how this behavior can be justified (or if 
> the plot is wrong).
> g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx 

How long is the sampling?  In the absence of -e and with -b being hidden from us 
for some unknown reason, it's hard to guess.  I'd say your simulation just isn't 
fully converged, although for complex systems that can be a challenge anyway. 
Nothing unusual.



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


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