[gmx-users] Re: Force a gromacs tool to write step-by-step a result in a result in a xvg file

[intra\sa175950]

Hi Florian, 

I have followed your suggestion below and used a pdb file instead of a xtc
file and it works!!! Thank you very much for the info.

A bientot 

Stephane 


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Message: 3
Date: Tue, 06 Sep 2011 12:26:34 +0200
From: Dommert Florian <dommert at icp.uni-stuttgart.de>
Subject: Re: [gmx-users] Force a gromacs tool to write step-by-step a
	result in a xvg file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1315304794.2757.18.camel at fermi>
Content-Type: text/plain; charset="utf-8"

Hi,

I would suggest you extract the single snapshot from your xtc file and
then run the analysis tool on the single snapshot file.


/Flo

On Tue, 2011-09-06 at 12:12 +0200, intra\sa175950 wrote: 
> Dear All 
> 
>  
> 
> I use the g_clustersize to examine the cluster decay vs. time during
> the aggregation process of glycolipids into a micelle with the
> following command:
> 
>  
> 
> $WORKDIR/gromacs-4.5.3/bin/g_clustsize_mpi -f *.xtc -s run_1.tpr -mc
> bDM-AMBER99SB-ILDN-Self_b_cluster.xvg -nc
> bDM-AMBER99SB-ILDN-Self_b_N_cluster.xvg -b 102000 -e 102000 -dt 4 -tu
> ps -n index.ndx
> 
>  
> 
> Unfortunately, the program stops with the following error after
> several steps 
> 
>  
> 
> -----
> 
>  
> 
> Program g_clustsize_mpi, VERSION 4.5.3
> 
> Source code file: matio.c, line: 561
> 
>  
> 
> Fatal error:
> 
> Lo: 0.000000, Mid: 1.000000, Hi: 1.000000
> 
> -----
> 
>  
> 
> I know that this error comes because I have in my system only one cluster
of constant size in my system.
> 
>   
> 
> Unfortunately, when this error appears g_clustsize_mpi stops and no
> results for the preceding steps are written in the corresponding xvg
> files.  So it is possible to force g_clustersize (and any others
> gromacs tools) to write step-by-step a calculation in a *.xvg file.
> 
>  
> 
> Thank you in advance for your help 
> 
>  
> 
> Stephane
> 
> 
> -- 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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