On Sat, Jun 18, 2011, Xioling Chuang wrote:
>
> As I understand, Amoeba force field has it own parameters for water and
> ions. If I want to use Amoeba for MD simulation of the system solvated
> in water and ions, should I use the common command like,
> - solvatebox dna TIP3PBOX 8.0
> - addions dna Na+ 0
> Also, should I load frcmod for TIP3P and for ions?
If you want to use the Amoeba force field, you need to use its parameters for
water and ions, *not* TIP3 water. Of course, you are certainly allowed to
experiment with whatever force field combination you like, but I don't think
what you propose is likely to yield results of very much interest.
...dac
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Received on Sat Jun 18 2011 - 06:00:03 PDT
