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

Henri Ervasti h.k.ervasti at tudelft.nl
Tue Jan 5 11:56:09 CET 2010

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.

Happy New Year! Best wishes,
Dr. Henri K. Ervasti 
Delft University of Technology 
Process & Energy Laboratory 
Leeghwaterstraat 44 k. 0.30 
2628CA Delft 

e-mail: h.k.ervasti at tudelft.nl 
phone: +31 (0)15 27 86662 
fax:   +31 (0)15 27 82460

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