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Hi,
<p>I've made a 3ns md run of a system consisting a protein, a small
ligand, water and some salt molecules.
<br>The backbone RMSD of the protein was stable during the first 2ns, with
a maximum value of 1.8nm. Most of the time the RMSD was ~1.5nm.
<br>After ~2ns, the RMSD started rising. It reached ~1.95ns at 3ns.
<p>My question is:
<br>1. Does this necessarily means that there's something wrong with my
simulation?
<br>2. If it doesn't, how can I verify it (i.e. how can I make sure that
the protein undergoes a some kind of a conformational change)?
<p>I'd appreciate any help,
<br>Ran.
<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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