Dear Christoph,
What does table.*xvg give me a sign for screwing up?
In the setting file, I have set min and max, 0 and 1.5 for all interactions
except for one A-D interaction.
I took a look at table*.xvg files in step016 (1 vs 6 columns), but nothing
strange. I drew all interactions and those looked fine.
I also increased iterations_max to 1000. But the same error at step004 (2
of the 900 bonded interactions could not be calculated because some atoms)
still came out.
Would picking different min and max help solve this error?
Thank you.
Best regards,
Changwoon Jang
On Tue, Jan 26, 2016 at 2:31 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-01-26 12:08 GMT-07:00 Chang Woon Jang <[email protected]>:
> > Dear Votca Users,
> >
> >
> > I have a simple question. I have run IBI for my own polymer system
> using
> > csg_inverse --option setting.xml following votca tutorials.
> >
> > When I first ran IBI in my desktop, the iterations stopped at Step 5 with
> > the following error.
> > -------------------------------------------------------
> > Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
> > Source code file:
> > /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec_top.c,
> line:
> > 394
> >
> > Fatal error:
> > 2 of the 900 bonded interactions could not be calculated because some
> atoms
> > involved moved further apart than the multi-body cut-off distance (1.5
> nm)
> > or the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and
> > tabulated bonds also see option -ddcheck
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > Then, I re-ran the same IBI without changing anything in setting.xml and
> > grompp.mdp files. It stopped 16 Step (Step 16) with error "1 of the 900
> > bonded ...". Is there a reason for this?
> Usually that means one of the tables is screwed up.
> Go in step_016 or step_005 and have a look at table.*xvg (column 1 vs
> column 6).
>
> Maybe you have to pick min and max differently or run longer per step
> for better statistics.
>
> Christoph
>
> >
> >
> > Thank you.
> >
> >
> > Best regards,
> > Changwoon Jang,
> >
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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