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wei-xin xu wrote:
<blockquote
cite="mid:d2ec8c310801091828q71dbe4dh34ab7d9657d2a8c5@mail.gmail.com"
type="cite"><span class="gmail_quote">2008/1/10, Mark Abraham <<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:</span>
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<p><font style="background-color: rgb(255, 102, 102);">Some hints on
practices that generally <b>not a good idea</b> to use: </font></p>
<ul>
<li><font style="background-color: rgb(255, 102, 102);">Do not use
separate thermostats for different components of your system. Some
molecular dynamics thermostats only work well in the thermodynamic
limit. If you use one thermostat for, say, a small molecule, another
for protein, and another for water, you are likely introducing errors
and artifacts that are hard to predict. In particular, do not couple
ions in aqueous solvent differently from that </font></li>
<li><font style="background-color: rgb(255, 102, 102);">solvent.</font>
</li>
</ul>
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<div><font style="background-color: rgb(51, 255, 255);">Sorry that I
do not actually understand here. The link I copied above shows that
better not to "couple ions in aqueous solvent differently from that
solvent". Maybe not separately but differently (mean different
temperature)?
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<div><font style="background-color: rgb(51, 255, 255);">I am actually
a novice in Gromacs.</font><br>
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</blockquote>
It's a bit off-topic.<br>
<br>
The paragraph quoted above implies that "not separately" so it is
generally applies to cases where you want to make a
temperature-coupling group of a small number of particles<br>
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