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

Yang Ye leafyoung at yahoo.com
Thu May 3 16:08:19 CEST 2007

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.

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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