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On 6/03/2012 10:40 PM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQEBE0wt5ZA1y8o0uPq0-M3TzzkuvE8sAvphMCs6JT-9BA@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Tue, Mar 6, 2012 at 11:35 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px
0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="HOEnZb">
<div class="h5">On 6/03/2012 8:21 PM, Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px
0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Dear
Gmx Users,<br>
I am running my protein with ligand. at the begining of
my simulation the protein is far away from the ligand.
Then in about 5-10 ns my ligand binds to the protein
surface remaining there for rest 90-95 ns. Would you
adjust coupling groups in thermostat as:<br>
a) Protein_LIg and Water_and_ions<br>
b) Protein Water_ions_LIG<br>
c) Protein LIG Water_ions<br>
<br>
</blockquote>
<br>
</div>
</div>
I'd consider a single coupling group before any of those. See
final part of manual 3.4.8 and ref therein. c) is unsound
because the ligand is likely too small. The lack of T-group
atom contiguity in a) might be an issue, I'm not sure. b) is
probably what people do, but you know this from your
literature searching about similar work, right? :-)</blockquote>
<div> </div>
<div>Well...I used a) approach as Ligand becaome a part of the
protein quite fast.</div>
</div>
</blockquote>
<br>
Sure, but if the path that took it there might be unsound, then you
can't refute the argument that the fact that that path occurred
might be a numerical artefact.<br>
<br>
<blockquote
cite="mid:CAKZJqQEBE0wt5ZA1y8o0uPq0-M3TzzkuvE8sAvphMCs6JT-9BA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> The b) just was my own tought as at the begining of the
simulation is in water only, however just for 500 ps as far as
I see out of 100ns. How would you tackle this?</div>
</div>
</blockquote>
<br>
Didn't I answer this already? :-)<br>
<br>
Mark<br>
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