<div dir="ltr"><div><font face="Arial">I have run the following command on the Cluster server and I got the following error. Can anyone Please help me why I am facing this error. </font><font face="Tahoma"></font></div><div><font face="Tahoma"></font><br></div><div><font face="Tahoma">gmx mdrun -deffnm nvt_2 -v<span style="color:black"></span></font>
</div><div><br></div><div>
</div><p class="MsoNormal"><span style="color:black;font-family:"Tahoma",sans-serif;font-size:10pt">Reading
file nvt_2.tpr, VERSION 5.0.4 (single precision)<br>Changing nstlist from 10 to
25, rlist from 1.4 to 1.433</span><span style="color:black"></span></p>
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<p class="MsoNormal"><span style="color:black;font-family:"Tahoma",sans-serif;font-size:10pt"><br>Will
use 108 particle-particle and 12 PME only ranks<br>This is a guess, check the
performance at the end of the log file<br>Using 120 MPI threads<br>Using 1
OpenMP thread per tMPI thread<br>starting mdrun 'Protein in water'<br>50000
steps, 100.0 ps.</span><span style="color:black"></span></p></div>
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<p class="MsoNormal"><span style="color:black;font-family:"Tahoma",sans-serif;font-size:10pt">-------------------------------------------------------<br>Program
gmx, VERSION 5.0.4<br>Source code file:
/share/apps/src/gromacs-5.0.4/src/gromacs/mdlib/pme.c, line:
7
54</span><span style="color:black"></span></p></div>
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<p class="MsoNormal"><span style="color:black;font-family:"Tahoma",sans-serif;font-size:10pt">Fatal
error:<br>2 particles communicated to PME rank 4 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in dimension
x.<br>This usually means that your system is not well equilibrated.<br>For more
information and tips for troubleshooting, please check the GROMACS<br>website at
<a href="https://uscmed.sc.edu/owa/redir.aspx?C=yM9xud_v1UCcNWWL-kM_GJgAd3dac9JI8UROBD4C7QFS8Rm-Bi1ts3jy27V4QHa_v159NARSf4A.&URL=http%3a%2f%2fwww.gromacs.org%2fDocumentation%2fErrors" target="_blank"><font color="#0000ff">http://www.gromacs.org/Documentation/Errors</font></a><br></span><br clear="all"></p></div><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div> regards, </div><div><br></div><div>Dr. Naidu</div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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