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On 12/26/2011 7:45 AM, Lara Bunte wrote:
<blockquote
cite="mid:1324845944.49502.YahooMailNeo@web29406.mail.ird.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
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<div><span id="result_box" class="" lang="en"><span class="hps">Hello</span><br>
<br>
<span class="hps">I have a few</span> <span class="hps">questions
about</span> <span class="hps">molecular</span> <span
class="hps">dynamics</span> <span class="hps">simulations.</span><br>
<br>
<span class="hps">1)</span> <span class="hps">For a
molecule</span> <span class="hps">Newton's</span> <span
class="hps">equation of motion</span> <span class="hps">is
solved</span><span>.</span> <span class="hps">Do I get
here one resulting force for the hole molecule or do I get
a lot of forces, one for each atom?</span><span
class="hps"></span><span class="hps"></span><br>
<br>
<span class="hps">2)</span> <span class="hps">The force is</span>
<span class="hps">calculated from</span> <span class="hps">the
potential.</span> <span class="hps">This</span> <span
class="hps">consists of the sum</span> <span class="hps">of
potentials</span> <span class="hps">linear</span> <span
class="hps">vibration</span><span class="">,</span> <span
class="hps">oscillation</span> <span class="hps">angle</span><span>,</span>
<span class="hps">torsional</span> <span class="hps">and
non</span><span>-binding parts</span> <span class="hps">as</span>
<span class="hps">Coulomb and</span> <span class="hps">Lennard</span><span
class="atn">-</span><span>Jones</span> <span class="hps">potential.</span><br>
<br>
<span class="hps">How do you calculate</span> <span
class="hps">the parameters for</span> <span class="hps">these
potentials</span><span>?</span> I heard something about QM
calculations but what do they how calculate?<br>
</span></div>
</div>
</blockquote>
<br>
The process by which each force field is parameterized differs, and
is best learned about by reading the original literature. References
may be found in the GROMACS manual.<br>
<br>
Mark<br>
<br />--
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