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My mdp file is what <a href="http://cs86.com/CNSE/SWNT.htm">http://cs86.com/CNSE/SWNT.htm</a> has. I used nose-hoover for Tcouple.<div>and the beginning of mdp code looks like:</div><div><br></div><div><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div><div>; Start time and timestep in ps</div><div>tinit = 0</div><div>dt = 0.0005</div><div>nsteps = 10000000</div><div>; For exact run continuation or redoing part of a run</div><div>init_step = 0</div><div>; mode for center of mass motion removal</div><div>comm-mode = Angular</div><div>; number of steps for center of mass motion removal</div><div>nstcomm = 1</div><div>; group(s) for center of mass motion removal</div><div>comm-grps =</div><div><br></div><div><br></div><div>I used gromacs 3.3.3 and in the vacuum. I applied the heat first around 10 layers.</div><div>after I finished my simulation and look at the edr file, the result temperatures are higher than what I gave. It looks like it generates heat by it self.</div><div>But when I do same simulation with less molecules such as 6000, it looks fine.</div><div><br></div><div><br></div><div><br><br><hr id="stopSpelling">Date: Tue, 9 Mar 2010 08:57:12 +1100<br>From: Dallas.Warren@pharm.monash.edu.au<br>Subject: RE: [gmx-users] large number of molecules<br>To: gmx-users@gromacs.org<br><br>
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<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:'Calibri','sans-serif';color:#1F497D">You are going to have to provide a lot more details than that if
you want some help.</span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:'Calibri','sans-serif';color:#1F497D"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:'Calibri','sans-serif';color:#1F497D">What is “wrong results”? What is your input (copy and paste
some commands in)? What is the output (copy and paste)? What makes you think
the results are “wrong”? In what situations are they “right”? … and there are
a lot more questions that could be asked ……</span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:'Calibri','sans-serif';color:#1F497D"> </span></p>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Calibri','sans-serif';color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style="font-size:10.0pt;font-family:'Calibri','sans-serif';color:#1F497D">Drug Delivery, Disposition and Dynamics</span><span style="font-size:10.0pt;font-family:'Calibri','sans-serif';color:#1F497D"><br>
</span><span style="font-size:10.0pt;font-family:'Calibri','sans-serif';color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:'Calibri','sans-serif';color:#1F497D">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style="font-size:11.0pt;font-family:'Calibri','sans-serif';color:#1F497D"> </span></p>
</div>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:'Calibri','sans-serif';color:#1F497D"> </span></p>
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<p class="ecxMsoNormal"><b><span style="font-size:10.0pt;font-family:'Tahoma','sans-serif'">From:</span></b><span style="font-size:10.0pt;font-family:'Tahoma','sans-serif'">
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>ksm tprk<br>
<b>Sent:</b> Tuesday, 9 March 2010 8:33 AM<br>
<b>To:</b> gromacs users<br>
<b>Subject:</b> [gmx-users] large number of molecules</span></p>
</div>
</div>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'">Hello,</span></p>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'"> </span></p>
</div>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'">I
simulate carbon nanotube and basically I follow up <a href="http://cs86.com/CNSE/SWNT.htm">http://cs86.com/CNSE/SWNT.htm</a></span></p>
</div>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'">But
when I increase the number of molecules (like 15000) , it gives me wrong
results.</span></p>
</div>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'">Do
you know why this is happen?</span></p>
</div>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'"> </span></p>
</div>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'">Thank
you,</span></p>
</div>
<div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'">Kasim</span></p>
</div>
<p class="ecxMsoNormal"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'"> </span></p>
<div class="ecxMsoNormal" align="center" style="text-align:center"><span style="font-size:10.0pt;font-family:'Verdana','sans-serif'">
<hr size="2" width="100%" align="center">
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