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<pre>Hi,</pre>
<pre>Does this approach still confer some advantages compared to normal MD?</pre>
<pre>For example, can I use non-periodic boundary conditions in order to reduce computation time?</pre>
<pre></pre>
<pre>Thanks,</pre>
<pre>Ran.</pre>
<p><br>Berk Hess wrote:
<blockquote TYPE=CITE>> > Regarding SD - is it possible to divide the system
to a region were full
<br>>MD takes place and a region where SD is effective?
<p>>we can not combine these.
<p>They can be combined.
<br>You can use different friction constants for different groups of atoms.
<br>A very small friction produces results which are almost indistinguishable
<br>from MD.
<br>The only problem is that you should not have to much cut-off artifacts,
as
<br>these might
<br>alter the temperature.
<br>But such an approach will not make the simulation faster, as the timestep
<br>will be limited
<br>by the MD part and unless the friction constant is very high, SD will
not
<br>allow for larger
<br>timesteps then MD.
<p>Berk.
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<pre>--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------</pre>
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