[gmx-users] gmx_clustsize

[Bratin Kumar Das]

Thanks for your reply

On Mon 20 May, 2019, 9:24 PM David van der Spoel, <spoel at xray.bmc.uu.se>
wrote:

> Den 2019-05-20 kl. 11:24, skrev Bratin Kumar Das:
> > Hi,
> >      I wan to calculate the size of oligomers formed during the course of
> > simulation. Therefore I used gmx clustsize. The command I used is given
> > below
> >   > gmx clustsize -f md-cntr.xtc -s extend9.tpr -n protein_index.ndx -nc
> > no_of_clust.xvg -ac avg_cluster_size -hc hist_clust.xvg -dt 100 -cut 0.6
> > -pbc -mol -b 0 -e 50000
> > The calculation is ended up with an error which is given below
>
> I think it means you have one cluster during the whole simulation. Note
> that periodic boundary conditions are taken into account.
>
> Try reducing the cut-off distance.
>
> > Back Off! I just backed up no_of_clust.xvg to ./#no_of_clust.xvg.2#
> >
> > Back Off! I just backed up avg_cluster_size.xvg to
> > ./#avg_cluster_size.xvg.2#
> >
> > Back Off! I just backed up maxclust.xvg to ./#maxclust.xvg.3#
> >
> > Back Off! I just backed up temp.xvg to ./#temp.xvg.3#
> > Reading frame       0 time    0.000   Reading file extend9.tpr, VERSION
> > 2016.5 (single precision)
> > Reading file extend9.tpr, VERSION 2016.5 (single precision)
> > Using molecules rather than atoms. Not reading index file
> protein_index.ndx
> > Last frame       5000 time 50000.000
> >
> > Back Off! I just backed up maxclust.ndx to ./#maxclust.ndx.1#
> > Total number of atoms in clusters =  13284
> > cmid: 1, cmax: 1, max_size: 13284
> >
> > Back Off! I just backed up csize.xpm to ./#csize.xpm.1#
> >
> > -------------------------------------------------------
> > Program:     gmx clustsize, version 2016.5
> > Source file: src/gromacs/fileio/matio.cpp (line 690)
> >
> > Fatal error:
> > Lo: 0.000000, Mid: 1.000000, Hi: 1.000000
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > Can any one help me out..what kind of error it is.
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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