[gmx-users] Bug in g_mindist version 3.3.1?

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 23 18:22:10 CEST 2006

Volker Knecht wrote:
> Dear all,
> there seems to be a bug in g_mindist version 3.3.1. When using g_mindist 
> to determine the minimal distance between two molecules in solution as a 
> function of time, the output fluctuates around 0.1nm although the 
> molecules are separated for part of the time. When using version 3.2.1 
> instead, the output is fine (separation on the nm range for part of the 
> time in agreement with visual inspection).
> Unfortunately, g_mindist version 3.2.1 gives the right output if it 
> runs, but in some cases crashes with a segmentation fault as reported in 
> the mailing list previously.  Therefore it would very helpful if the 
> apparent bug in version 3.3.1 could be fixed.
> Thanks in advance.
> Kind regards,
> Volker
Are you certain it is not due to periodic boundary conditions, i.e. te 
distance is reallly correct if PBC are taken into account?

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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