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On 3/01/2012 6:54 AM, Alex Jemulin wrote:
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cite="mid:1325534044.73574.YahooMailNeo@web132401.mail.ird.yahoo.com"
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<div>Dear all</div>
<div> </div>
<div>I run a MD on a GPCR (transmembrane protein)</div>
<div>Then I run a PCA on results and I found 3PC sufficient to
explain variance.</div>
<div>On the same PC I get big values for samples located both at
Nter (extracellular) and Cter (intracellular) or for similar
cases such as both Nter(extracellular) and Loop5
(intracellular).According to you how could I explain the
motion of group atoms intra and extracellular on the same
components? </div>
<div>Does it mean the motion of some atoms at Nter (for
instance) could influence the motion at Cter ? Could it be
logic?</div>
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<br>
Highly unlikely. You don't give any details of your simulation, so
your simulation could be too short, or have insufficient distance
between your periodic images.<br>
<br>
Mark<br>
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