[gmx-users] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster

Jan Riehm jriehm at bioinformatik.uni-saarland.de
Wed May 27 17:11:54 CEST 2015

Dear users,

I am using the amber99sb-ildn.ff force field to simulate an adrenodoxin 
molecule in a water box. In it there is a 2Fe2S cluster which is 
covalently bound to four surrounding cysteines (two cysteines to each Fe 
atom). After the first equilibration step (nvt) one of the cysteines 
clashes or overlaps with the farther apart Fe atom (which is not 
covalently bound). I've checked for the nonbonded interaction values in 
the ffnonbonded.itp and the values (sigma and epsilon) for Fe are zero 
in the [atomtypes]-directive.

I am pretty new to this MD simulation stuff and want to know how to 
derive the values for epsilon and sigma. Or can I look them up anywhere? 
Any hint to a tutorial would be very helpful!

Thank you very much and best regards,


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