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<pre>If it was possible, I'd like to simulate my system for around 100ns. However, this is too complex for me now, as I just want to test a hypothesis.</pre>
<pre>Ran.</pre>
<p><br>David van der Spoel wrote:
<blockquote TYPE=CITE>On Tue, 2003-12-09 at 15:00, Ran Friedman wrote:
<br>> Dear GMX users and developers,
<br>> I'd like to simulate protein motions which will normally take longer
than the scale of MD simulations.
<br>> Are such calculations feasible using the SD or BD algorithms in Gromacs?
<br>> Are you aware of any references to such calculations made using Gromacs?
<br>> Regarding SD - is it possible to divide the system to a region were
full MD takes place and a region where SD is effective?
<p>we can not combine these. how long would you like to simulate? 50 -
100
<br>ns is not a real problem ig you have a few dedicated linux boxes.
<p>> Thank you,
<br>> Ran.
<br>> --
<br>> ------------------------------------------------------
<br>> Ran Friedman
<br>> Laser laboratory for fast reactions in biology
<br>> Department of biochemistry
<br>> Faculty of life sciences
<br>> Tel-Aviv university
<br>> 972-3-6409824
<br>> ------------------------------------------------------
<br>>
<br>--
<br>David.
<br>________________________________________________________________________
<br>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596,
75124 Uppsala, Sweden
<br>phone: 46 18 471 4205
fax: 46 18 511 755
<br>spoel@xray.bmc.uu.se spoel@gromacs.org
<a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a>
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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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