[gmx-users] RDF plot. This is weird!

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 9 21:01:56 CET 2009

Lum Nforbi wrote:
> Dear all,
>  I have attached a RDF plot of 2000 molecules of water (SOL is the 
> system name). It does not follow the normal trend. I used the command 
> line below to get this plot:
> g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg
> The run took about 1h 45 min to be complete.
> The plot does not follow the normal trend I see for rdf plot ie first 
> peak higher than the second, so I know something is wrong but I don't 
> know what. Can someone take a look at my graph and tell me what is wrong 
> with my system or with my computation?

What did you choose as the input groups to be analyzed?  How long was your 



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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