[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3
lastexile7gr at yahoo.de
Tue Mar 3 17:33:52 CET 2009
this has to do with my personal experience of using Gromacs version 4.0.3. So this is not an official response.
While I was trying to run an NVT simulation in a monoclinic box I encountered the following problem:
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
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 following:
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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