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On 28/04/2012 10:54 AM, Ho, Tuan A. wrote:
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<p class="MsoNormal"><span style="color:#1F497D">Thank Mark,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">I
freeze the SOL because I would like to check if it is
because of SOL bad contact.</span></p>
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<br>
You can't do a dynamical simulation with zero degrees of freedom.<br>
<br>
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<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">
However, it turns out that the graphite deformation is the
problem.
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Under what conditions? Your earlier simulation probably blew up
because of the above.<br>
<br>
Mark<br>
<br>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">My friend asks
me to use only one processor, and it is running well (no SOL
freeze). Hopefully, after I got the final configuration for
serial run, I will be able to perform a parallel simulation.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thank you so
much.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Any idea for
this problem is highly appreciated since I am not sure if I
will be able to perform a parallel job.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Tuan.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Friday, April 27, 2012 6:36 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] SWM4_DP water on
graphite surface<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: <o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif"">Dear Gromacs users,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif"">I would like to
simulate a thin film of SWM4_DP water on graphite surface.
First, I equilibrate the water only (run very well), then I
add a graphite surface on it. I freeze the graphite surface
but the graphite surface acted crazily after a few time step
(graphite surface deform critically, “blow”). The error is
</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Step
140:</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">The
charge group starting at atom 266 moved than the distance
allowed by the domain decomposition (1.000000) in direction
Z</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">distance
out of cell 1.038218</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Old
coordinates: 0.123 2.627 6.000</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">New
coordinates: 0.013 0.671 11.038</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Old
cell boundaries in direction Z: 5.978 10.000</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">New
cell boundaries in direction Z: 5.660 10.000</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">-------------------------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Program
mdrun, VERSION 4.0.7</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Source
code file: domdec.c, line: 3654</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Fatal
error:</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">A
charge group moved too far between two domain decomposition
steps</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Courier New"">This
usually means that your system is not well equilibrated</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif"">I don’t understand
why I freeze the graphite surface but the carbon atom moved
around. If it is because of bad contact, I think the water
should be blown instead of carbon atom</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif""> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif ;","serif"">I ran the SPC/E
water model on graphite very well.
</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><br>
Probably you didn't use freezedim on the SOL degrees of
freedom when you used that water model, as you have here.<br>
<br>
Mark<br>
<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif"">I attached the mdp
file, the topology file.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif""> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif"">Please let me know if
I did anything wrong.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif"">Thanks in advance.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif"">Tuan.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman , serif","serif""> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><o:p> </o:p></span></p>
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