[gmx-users] g_clustsize bug ( (fwd)

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 13 14:41:21 CET 2009

Alessandro Magliano wrote:
> Dear GROMACS users and developers,
> I am writing to ask for some help with using g_clustsize.
> I have used g_clustsize with the following command line:
> g_clustsize_d -f traj_no_water.xtc -s conf_no_water.tpr -mol -cut 0.3 
> -dt 1000
> 'traj_no_water.xtc' contains the trajectory of an ensemble of 26 
> identical peptides simulated in water;
> 'conf_no_water.tpr' contains the topological information of the peptide 
> structure.
> The output file csize.xpm, which contains the clusters size 
> distribution, appears to be wrong. In particular, it shows the formation 
> of clusters of every possible size at the same time ( from 1 molecule to 
> 26 molecules, in my specific case), even though this is not consistent 
> with the total number of molecules present in the system.
> This bug is present in all the Gromacs versions I tried out: 3.0.3, 
> 3.1.4, 3.2.1, 3.3.2, 3.3.3 and 4.0.2.
> I should be grateful if anyone could tell me how to overcome this problem.
Do you mean that

Sum_i N_i * i != Nmol?

> Thanks in advance.
> Alessandro Magliano
> Dr.Alessandro Magliano
> PhD Student
> Department of Chemistry
> University of Rome "Sapienza"
> Rome
> Italy
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David van der Spoel, Ph.D., Professor of Biology
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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