On Fri, Aug 05, 2011, li he wrote:
> I am trying to calculate the solvation energy of Na+ in water with
> thermodynamics integration implemented in amber11, sander.
> I copied parameters from ponder's webpage to
> amber11/dat/leap/parm/amoebapro.prm, created a Na+ offlib file by taking
> data from
> amber11/dat/leap/lib/ions08.lib and change the atom type from "Na+" to 205,
> as the original amoeba forefield in amber11 does not
> have Na+'s parameters.
> when I calculated the energy cost to turn on the charge of amoeba Na+, I
> found the DV/DL is alyways 0.
I think you are correct here: TI is not implemented for the amoeba force
field. Certainly none of the softcore stuff will work. Some interested
person (Pengyu?) is needed to keep the amoeba implementation going forward.
....dac
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Received on Sat Aug 06 2011 - 13:30:03 PDT
