On Thu, Oct 21, 2010, Andrew Jewett wrote:
>
> Is sander able to simulate covalently bonded periodic infinite crystals?
> I worry that sander will get confused whenever a covalent bond crosses
> the periodic boundary.
You are correct: the Amber codes are not designed for periodic infinite
crystals: specifically, bonds cannot cross periodic boundaries. Also, not
that unit cell dimensions must be more than twice the non-bonded cutoff, so
small unit cells are not feasible.
[The first problem, with bonds, is probably not all that hard to fix. But one
would still have the need for a large unit cell, and that would require major
surgery to change.]
....dac
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Received on Fri Oct 22 2010 - 05:30:06 PDT
