[gmx-users] Re: Re: g_clustsize bug

[David van der Spoel]

Alessandro Magliano wrote:
> Dear Prof. van der Spoel,
> I ran g_clustsize_d again with the following command line:
> g_clustsize_d -f traj_no_water.xtc -s conf_no_water.tpr -mol -dt 1000 
> -cut 0.25 -nlevels 26
> Attached you will find the csize in pdf format.
> The csize file shows that clusters with size from 1 to 25 molecules are 
> present at the same time (timeframe) along the whole simulation time, 
> which is clearly physically impossible.

Please submit a bugzilla with sample input files (short ones please).
I'm not quite sure I understand what is going on though.

> 
> Thank you.
> 
> Best wishes
> 
> Alessandro Magliano
> 
> 
> 
> Da:  David van der Spoel <spoel at xray.bmc.uu.se>
> To:  Discussion list for GROMACS users <gmx-users at gromacs.org>
> Reply-To:  Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date:  13 gen 2009, 14:41:21
> Subject:  Re: [gmx-users] g_clustsize bug ( (fwd)
> 
> 
> 
> ---------------------------------------------------------------------------- 
> ----
> 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.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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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