[gmx-users] Wrong bond and Lennard-Jones potentials in cyclohexane

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 5 12:22:21 CET 2010

Henri Ervasti wrote:
> Dear all,
> Thank you for your help and comments on abovementioned problem. In the
> end though it turned out that the large potentials were caused by
> overlapping rings (two rings were going through inside each other) which
> genbox unfortunately somehow had generated. I hadn't though of that
> myself until a colleague made a remark that this might be the case. I
> used genconf to do another simulation box, where there is no chance of
> this happening, and my results turned out rather good.

Unlucky! Still, it underscores the old story that one needs to visualize 
results to check they follow one's preconceptions. In extremis, with 
ring structures, use genconf with a dummy space-filling atom that you 
edit out later.


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