Dear,<div><br></div><div>I create a box of water with 10 MIBC molecules on two opposite surfaces.</div><div>then I used the command "<span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; ">grompp -f input_min.mdp -o min.tpr -c box1.g96" to creat .tpr file before using the command "genion -s min.tpr -o add.gro -nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ and 20 Cl- into this box.</span></div>
<div><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">I run the command "grompp -f input_min.mdp -o min.tpr -c add.gro" again and appeared the warings :</span></font></div>
<div><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></div><div><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;"><div>
<font class="Apple-style-span" color="#CC0000">Warning: atom name 176 in topol.top and add.gro does not match (CL - OW)</font></div><div><font class="Apple-style-span" color="#CC0000">Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1)</font></div>
<div><font class="Apple-style-span" color="#CC0000">Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2)</font></div><div><font class="Apple-style-span" color="#CC0000">Warning: atom name 179 in topol.top and add.gro does not match (CL - OW)</font></div>
<div><font class="Apple-style-span" color="#CC0000">Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1)</font></div><div><font class="Apple-style-span" color="#CC0000">(more than 20 non-matching atom names)</font></div>
<div><font class="Apple-style-span" color="#CC0000"><br></font></div><div><font class="Apple-style-span" color="#CC0000">WARNING 1 [file topol.top, line 72]:</font></div><div><font class="Apple-style-span" color="#CC0000"> 21754 non-matching atom names</font></div>
<div><font class="Apple-style-span" color="#CC0000"> atom names from topol.top will be used</font></div><div><font class="Apple-style-span" color="#CC0000"> atom names from add.gro will be ignored</font></div><div><font class="Apple-style-span" color="#CC0000">......</font></div>
<div><div><font class="Apple-style-span" color="#CC0000">Fatal error:</font></div><div><font class="Apple-style-span" color="#CC0000">Too many warnings (2), grompp terminated.</font></div><div><font class="Apple-style-span" color="#CC0000">If you are sure all warnings are harmless, use the -maxwarn option.</font></div>
</div><div><br></div><div>then I tried with the command "grompp -f input_min.mdp -o min.tpr -c add.gro -maxwarn 2000" and it run well.</div><div><br></div><div>However, when I kept working with the command "mdrun -s min -o min -c min.g96 -x min -e min -g min", the errors appeared as follow:</div>
<div><br></div><div><div><font class="Apple-style-span" color="#CC0000">Fatal error:</font></div><div><font class="Apple-style-span" color="#CC0000">3 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.</font></div>
<div><font class="Apple-style-span" color="#CC0000">This usually means that your system is not well equilibrated.</font></div><div><font class="Apple-style-span" color="#CC0000">For more information and tips for troubleshooting, please check the GROMACS</font></div>
<div><font class="Apple-style-span" color="#CC0000">website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></font></div></div><div><br></div><div>Please help me to fix this problem.</div>
<div><br></div><div>Many thanks.</div><div><br></div><div><span class="Apple-style-span" style="font-family: arial; font-size: small; "> </span></div></span></font><div>Nguyen Van Cuong</div>
<div>PhD student - Curtin University of Technology</div>
<div>Mobile: (+61) 452213981</div>
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