[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck

[gromacs query]

>> You can probably confirm that from the time series of some observables.

In the end of log file it complains about these two atoms:

the first 10 missing interactions, except for exclusions:
                Bond atoms   94  177           global    94   177
                Bond atoms   97  177           global    97   177


I checked these two atoms and visually they look fine and whole system
behaves nicely. I am not sure, what observables I can measure?

I restarted the job its running without error. I got this error when
protein was in edge of the box though in PBC it makes no sense to say like
that.

I have one silly query, why always in such cases when I simulate something
with membrane my protein loves to stay always in the edge of box? I mean,
If you visualise in VMD non-imaged trajectory. (Though I understand in PBC
there is no edge).

regards,
Jiom

On Mon, Mar 9, 2015 at 5:23 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Very likely your run is blowing up from (long-time) instability - two atoms
> have moved some crazy amount. You can probably confirm that from the time
> series of some observables.
>
> Mark
>
> On Mon, Mar 9, 2015 at 12:54 PM, gromacs query <gromacsquery at gmail.com>
> wrote:
>
> > Hi All,
> >
> > I am doing CG membrane with protein. After running long simulation I am
> > getting this error:
> >
> > Fatal error:
> > 2 of the 13319 bonded interactions could not be calculated because some
> > atoms involved moved further apart than the multi-body cut-off distance
> > (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for
> > pairs and tabulated bonds also see option -ddcheck
> > For more information and tips for troubleshooting, please check the
> GROMACS
> >
> >
> >
> > I could not find this on google. Should I restart with something like
> -rdd
> > 2 or so? I am just wondering how it will influence my overall
> calculations?
> > I think it will reduce ns/day? or is there any serious energy related
> > issues?
> >
> > Thanks,
> > JIom
> > --
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