[gmx-users] Lennard-Jones Rdf plot

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 5 20:09:47 CET 2010

Lum Nforbi wrote:
> Dear all,
>    Please, could someone tell me what could be the problem with the 
> attached LJ plot?
> Could it be due to wrong assignment of periodic boundary conditions?

First, do not attach files without file extensions.  For those of us who are 
security-conscious (some say "paranoid"), we won't open it.  It is much more 
useful to post an image file to some public site, like Photobucket or Google Docs.

Second, there is likely no way anyone can diagnose your problem unless you post 
a very detailed description of what you're doing.  You mention an "LJ plot" but 
the file name of your attachment would suggest a radial distribution function. 
What is it that you are trying to analyze?  How did you produce the plot?  Is it 
indeed an RDF?  If so, what was simulated, and for how long?  What were your 
.mdp parameters?  It is very doubtful that PBC alone caused issues, but rather 
your incorrect assignment of, e.g., cutoffs or some other feature.  But we don't 
know any of this yet.

Remember, we can't get inside your head to know what you're doing.  You've got 
to make it easy for us.


> Thank you,
> Lum


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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