[gmx-users] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster
jriehm at bioinformatik.uni-saarland.de
Wed May 27 17:11:54 CEST 2015
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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