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On 11/01/2012 4:23 PM, Tsjerk Wassenaar wrote:
<blockquote
cite="mid:CABzE1Sh3FUES9b9+6RXCybfhNawe_7G0-oeZSoKB1W7Jq8Bo8g@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Clarifying - the amount of noise is *inversely* related to the
number atoms. That should be fairly moot, though, because a
T-coupling group with less than a thousand atoms is probably not
worth considering. The algorithms work best in macroscopic limits,
so a group that's not at least 10% of your system is likely not
approaching that limit - and grompp will warn you about that.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CABzE1Sh3FUES9b9+6RXCybfhNawe_7G0-oeZSoKB1W7Jq8Bo8g@mail.gmail.com"
type="cite">
<p>Hope it helps,</p>
<p>Tsjerk</p>
<blockquote type="cite">On Jan 11, 2012 12:00 AM, "Mark Abraham"
<<a moz-do-not-send="true"
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:
>
>
>
> Steven Neumann wrote:
>>
>>
>>
>> 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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href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-u.">http://lists.gromacs.org/mailman/listinfo/gmx-u.</a>..</font></p>
</blockquote>
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