On Tue, Oct 07, 2014, Neha Gandhi wrote:
>
> I am interested in simulating a protein in a nonaqueous solvent box
> (specifically, chloroform). I am aware that AMBER provides a
> pre-equilibrated chloroform box, but am interested in knowing how AMBER
> treats counterions in the presence of such non-aqueous solvents.
I'm not aware of any testing of Amber ion parameters with chloroform. So you
might want to some simple liquid simulations (no protein) first to see what
happens.
> Do I need to add counterions to my box in the presence of protein and
> chloroform?
No, this is not required.
....dac
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Received on Tue Oct 07 2014 - 05:00:02 PDT
