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

David van der Spoel spoel at xray.bmc.uu.se
Thu May 3 16:59:23 CEST 2007

Yang Ye wrote:
> I hoped that they were 3 times but it isn't. For 40nm cube box, I have 
> maximum at 19.7nm for both -pbc and -nopbc.

these changes are only in the CVS latest version, not in the 3.3 branch.
> On 5/3/2007 6:44 PM, David van der Spoel wrote:
>> 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?
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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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