[gmx-users] Potential Energy = nan

Frederic Leroy frederic.leroy at urv.net
Thu Jun 30 05:27:48 CEST 2005


>I have a polymer chain grafted on a surface and do energy minimization (steepest
>descent) . when I take no interaction between surface and chain everything
>works fine. When I use van der wall interaction between surface and the chain
>after the energy minimization I get
>Potential energy = nan 
>What does this mean? can I continue an mdrun after having this message or
>something goes wrong
>Argyris Karatrantos
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>gmx-users at gromacs.org
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this sounds wrong because NaN generally means "Not A Number". There is 
certainly an interaction energy that is so huge that the result is out 
of the calculation capacity of the computer which then says "NaN". I 
mean, your chain is certainly overlapping the wall as far as VDW 
interactions are concerned. I would say you can not continue because you 
can not calculate with quantities that are not numbers!
Maybe somebody has better ideas...


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