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I'm sorry - that was a typo. All vlaues should be in Angstroms.
<p>Ran.
<p>David van der Spoel wrote:
<blockquote TYPE=CITE>On Thu, 2003-11-06 at 10:33, Ran Friedman wrote:
<br>> Hi,
<br>>
<br>> I've made a 3ns md run of a system consisting a protein, a
small
<br>> ligand, water and some salt molecules.
<br>> The backbone RMSD of the protein was stable during the first 2ns,
with
<br>> 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
<br>> simulation?
<br>> 2. If it doesn't, how can I verify it (i.e. how can I make sure that
<br>> the protein undergoes a some kind of a conformational change)?
<br>>
<p>Are you sure it's 1.5 nm? That sounds ridiculously high. Otherwise I've
<br>seen conformational changes happen after 50 ns, so anything is
<br>possible...
<p>> I'd appreciate any help,
<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>--
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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
------------------------------------------------------</pre>
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