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
------------------------------
Message: 3
Date: Tue, 06 Sep 2011 12:26:34 +0200
From: Dommert Florian <domm...@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@gromacs.org>
Message-ID: <1315304794.2757.18.camel@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: domm...@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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