[gmx-users] Iron containing structure simulation crash

Nikolaos Michelarakis nm884 at york.ac.uk
Tue Aug 12 18:27:42 CEST 2014

>An output coordinate file is always produced unless mdrun completely fails
>seg faults.  That doesn't mean the coordinates are sane.  It's meant to
help you
>diagnose in cases like this where you have an absurd force on some atom.

>What is atom 2832?  What's around it?  Is there anything obviously
clashing with
>it?  Also check the topology for errors.


The atom is the iron that I introduced. It is bound to an oxygen which is
itself bound to the carbon of a ring. It is found on the spot where the
ligand, not introduced in the simulation yet, is binding to the protein.
There are a few carbons and nitrogens but nothing in close proximity or
clashing with it.
The topology seems ok to me. This is the link to the file, the iron shows a
charge of +3, could this be the cause of such a great force?


Thank you again,


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