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On 24/11/2011 8:16 PM, cuong nguyen wrote:
<blockquote
cite="mid:CAMj9MaehC=pJewD=QBYnzENx6g2AA6XN6o5BfnZRhCBSm9pY+Q@mail.gmail.com"
type="cite">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>
</span></font></div>
</blockquote>
<br>
No, it ran poorly, because you didn't understand what you were doing
with -maxwarn. Your atom ordering must match between the .top and
.gro files. Ignoring the warning doesn't fix the problem.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAMj9MaehC=pJewD=QBYnzENx6g2AA6XN6o5BfnZRhCBSm9pY+Q@mail.gmail.com"
type="cite">
<div><font class="Apple-style-span" face="Helvetica" size="3"><span
class="Apple-style-span" style="font-size: 12px;">
<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 moz-do-not-send="true"
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>
<div> </div>
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</blockquote>
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