Dear Balazs
> how many atoms should be consider in the QM region?
This is really a difficult question to answer. In an ideal world you would
make the QM region as big as possible in order to minimise boundary effects.
However, the cpu time required goes up very rapidly with the number of QM
atoms so you need to make a tradeoff between the ideal situation and one
that is computationally manageable. Typically, on a single cpu machine the
maximum size QM region you will be able to handle would be around 50 atoms
or so. If you can run in parallel then you can use a much bigger QM region
but the Amber 8 QM code does not support this.
All the best
Ross
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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Received on Fri Aug 19 2005 - 19:53:01 PDT
