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<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Dear Gromacs users,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","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 <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">Step 140:<o:p></o:p></span></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<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">distance out of cell 1.038218<o:p></o:p></span></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<o:p></o:p></span></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<o:p></o:p></span></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<o:p></o:p></span></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<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">-------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">Program mdrun, VERSION 4.0.7<o:p></o:p></span></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<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">Fatal error:<o:p></o:p></span></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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New"">This usually means that your system is not well equilibrated<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">I ran the SPC/E water model on graphite very well.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">I attached the mdp file, the topology file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Please let me know if I did anything wrong.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Thanks in advance.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"">Tuan.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
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