[gmx-users] gmx_clustsize

[David van der Spoel]

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