[gmx-users] Re: Re: g_clustsize bug

[Alessandro Magliano]

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.

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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