<p>Hey,</p>
<p>In addition to the foregoing...<br>
The separate coupling is to prevent draining energy from one part to the other. It is pretty unlikely that either protein or tube will drain the other one. Water is always a different story. <br>
You can check the setup you choose afterwards, like after a short run, by rerunning the sinulation with the split groups and checking the temperature. E.g. if you run with protein and tube in one group, the should both end up having the same temperature, within the noise. Do mind the noise is related to the number of atoms in a group.</p>
<p>Hope it helps,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Jan 11, 2012 12:00 AM, "Mark Abraham" <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br><br><p><font color="#500050">On 11/01/2012 6:52 AM, Justin A. Lemkul wrote:
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> Steven Neumann wrote:
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>> On Tue, Jan...</font></p>
One alternative is to pay attention to the advice at the end of section 3.4.8 of the manual and ref cited there - that separate T-coupling groups can be worse than the problems they purport to fix.<font color="#888888"><br>
<br>
Mark</font><p><font color="#500050">
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