[gmx-users] Error with bonded interactions

[Mark Abraham]

Hi,

That'd generally mean your model was unstable. How does it go on on simple
systems e.g. one molecule in vacuum?

Mark

On Sun, Dec 13, 2015 at 1:54 AM Pallavi Banerjee <
pallavisept at students.iiserpune.ac.in> wrote:

> Hello all,
>
> My system is a coarse-grained polymer in vacuum and I provide bonded
> potentials in a tabulated format. After a run of about 10-15 ns, the
> following error shows up:
>
> 2 of the 146 bonded interactions could not be calculated because some atoms
> involved moved further apart than the multi-body cut-off distance (1.54773
> nm) or the two-body cut-off distance (2 nm), see option -rdd, for pairs and
> tabulated bonds also see option -ddcheck
>
>
>
> On having looked at  the trajectory, the system looked just fine.
> Even on using -noddcheck, the same error shows up after a few steps. How do
> you circumvent this?
>
> Many Thanks!
>
> -Pallavi Banerjee
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>