Serdar.<br><br>If the "real charge" of your system is not zero and you are using PME, then PME code will take account for any non-zero charge on the system and neutralize it with an uniform background charge (<a href="http://wiki.gromacs.org/index.php/Errors">http://wiki.gromacs.org/index.php/Errors</a>).<br>
If your system is composed by a protein, then try first to check the charge for every residue (maybe you found some aminoacid with a not integral charge).<br>Please note that several times if your charge is very close to an integer, this warning is generated as consequence of the " summation of many floating point numbers", check this link:<br>
<a href="http://www.gromacs.org/pipermail/gmx-users/2008-May/034092.html">http://www.gromacs.org/pipermail/gmx-users/2008-May/034092.html</a><br><br>However, your error is on the 3rd digit (by a magnitude of .004), on my experience gromacs "round errors" are very close to the integer (e.g. Sytem Charge = .9999998 or 1.000002), then I recommend you to take a look on your system.<br>
<br>Daniel<br><br><div class="gmail_quote">2008/7/10 serdar durdagi <<a href="mailto:durdagis@yahoo.de">durdagis@yahoo.de</a>>:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p>Dear all,</p>
<p> </p>
<p>In one of my simulations, total charge of the system is a noninteger number (like +15.996). I neutralized it with 16 chlorine atoms. I am using periodic boundary conditions. If I use the charge as it is, is it means infinite negative total charge on the system?</p>
<p> </p>
<p>Actually, when I check the simulation output parameters, it seems every thing okay..I am just curious if it's some thing wrong..</p>
<p> </p><font color="#888888">
<p>Serdar</p></font></td></tr></tbody></table><br><div class="WgoR0d">
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