[gmx-users] g_clustsize bug ( (fwd)

Alessandro Magliano a.magliano at caspur.it
Tue Jan 13 14:27:06 CET 2009

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 

'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 

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. 

Thanks in advance. 

Alessandro Magliano 


Dr.Alessandro Magliano
PhD Student
Department of Chemistry
University of Rome "Sapienza"

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