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<tt>Well, that's not very encouraging, but it's better than being wrong!</tt><tt></tt>
<p><tt>Thanks a lot,</tt>
<br><tt>Ran.</tt>
<p>Berk Hess wrote:
<blockquote TYPE=CITE>>Does this approach still confer some advantages
compared to normal MD?
<br>>
<br>>For example, can I use non-periodic boundary conditions in order to
reduce
<br>>computation time?
<p>No, it does not.
<br>If you would want to use non-periodic boundary conditions you would
need to
<br>restrain the outer shell
<br>of solvent atoms, which introduces artifacts. A boundary layer is required
<br>to minimize the effect of
<br>these artifacts.
<br>In the end it is computationally cheaper to use a periodic system in
a
<br>rhombic dodecahedron box.
<p>Berk.
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<pre>--
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Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
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