[gmx-users] g_dist producing inconsistent values

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 7 19:35:55 CET 2008

chris.neale at utoronto.ca wrote:
>> I've since found the source of my problem - the program was measuring 
>> the (marginally shorter) distance across the PBC boundary, rather than 
>> the distance
>> within the box.  Unfortunately there doesn't seem to be a way to turn 
>> PBC images off (correct me if I'm wrong?), so I guess I'm going to do 
>> some jiggerypokery with the data and some math.
Distance larger than half a box size are ill-defined anyway in a PBC 
simulation. In some special cases you can do this, for instance within a 
protein it would work. I've implemented -nopbc options in some programs 
but not in g_dist yet. Please put it on the developer wishlist. on the wiki.

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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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