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Posted By: jb007 Metal params - 10/09/03 11:35 AM
What's the rationale for choosing L-J parameters for metals? -
On comparison with Ne (rmin/2 = 1.53) in the CHARMM27 prm file with the nonbonded contact distance in the periodic system things look ok. However, for other metals, e.g. zinc, this trend is not obvious, rather it seems a bit ad hoc...so my question actually boils down to: To what extent should we use experimental values in defining force-field parameters?
Posted By: alex Re: Metal params - 10/14/03 12:08 AM

Parameters for ions are typically based on reproduction of the experimental
free energy of solvation. In Charmm, the ion is assigned a formal charge
and then the LJ parameters are optimized to reproduce the free energy
of solvation. There is a Beglov and Roux paper in which they did this
for sodium. Finally, it should be noted that one set of LJ parameters for
an ion may not yield proper interactions with all types of functional
groups. A trick to get around this in charmm is the use of NBFIX for
to assign specific ion-atom LJ parameters that balance such
interactions.

alex
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