[gmx-users] Error with bonded interactions
mark.j.abraham at gmail.com
Sun Dec 13 03:56:43 CET 2015
That'd generally mean your model was unstable. How does it go on on simple
systems e.g. one molecule in vacuum?
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
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