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 <sp...@xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Date: 13 gen 2009, 14:41:21
Subject: Re: [gmx-users] g_clustsize bug ( (fwd)
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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
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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