[gmx-developers] proposed change to g_rdf with -nopbc

David van der Spoel spoel at xray.bmc.uu.se
Thu May 3 12:44:20 CEST 2007

Yang Ye wrote:
> My system has an extensible rod-like structure which may elongate more 
> than half the diagonal distance. It is then desirable for g_rdf to count 
> this distance with -nopbc. I believer that g_rdf actually get this 
> distance but because it is out of the cut-off distance, it doesn't get 
> counted. To be consistent, -nopbc shall have a (possible) longest 
> cut-off distance for RDF calculation. Because max_cutoff2() doesn't 
> return such long distance, I add the code to get the diagonal length.
I just put an update to the code in CVS. But the cutoff used with -nopbc 
was and is 3 times the largest box edge. That should suffice for you 
shouldn't it?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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