[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Berk Hess gmx3 at hotmail.com
Wed Mar 4 09:23:52 CET 2009


Your solution seems to indicate that your system is unstable.
My guess is that your system was not well equilibrated and at some point
some non-bonded interactions were at a distance of more than cut-off+tab_ext.
That would make your system explode. In that case increasing tab_ext to 2 nm
should also suffice.


Date: Tue, 3 Mar 2009 08:33:52 -0800
From: lastexile7gr at yahoo.de
To: gmx-users at gromacs.org
Subject: [gmx-users] How to overcome Fatal error of bonded interactions	Gromacs 4.0.3


this has to do with my personal experience of using Gromacs version 4.0.3. So this is not an official response.

The story:

While I was trying to run an NVT simulation in a monoclinic box I encountered the following problem:

Fatal error:
25 of the 336080 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.895 nm) or the two-body cut-off distance (0.895 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck

and the:
Not all bonded interactions have been properly assigned to the domain decomposition cells

Trying to put aside the fact that my system had any bug I found in the net the

In order to overcome this error I increased the value of
table-extension          = 30
in my mdp file in such a way, as to be bigger from my biggest dimension I had in my system. The ran proceeded (until now that I'm writing this e-mail) without any problem.

This value has to do with the cut-off of pairs1-4 LJ interactions and is calculated in nm.


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