On Mon, Jun 11, 2018, 赵东波 wrote:
> Recently I am trying to use Amber to simulate a water box with 64 or 128
> molecules using the TIP3P or TIP4P etc. However, I failed because the
> cutoff is the main problem.
> So I am wondering if there is a way to overcome this porblem. I know
> that the TINKER program can do this and I don't know how they treat the
> cutoff problem.
You are correct: Amber requires the box size to be at least twice the
cutoff distance plus a "skin width" (specified by the skinnb variable).
In practice this means a minimum box size (in each dimension) of about
18 Å. This implies a minimum number of waters of about 200.
Like you , I don't know the details of how Tinker addresses such
simulations.
....dac
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Received on Mon Jun 11 2018 - 05:00:02 PDT
