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<TITLE>functionalized surface: counter ions ? PME or RF</TITLE>
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<P><FONT SIZE=2 FACE="Arial">Hello everyone,</FONT>
<BR><FONT SIZE=2 FACE="Arial">I would appreciate some advice on my simulation.</FONT>
<BR><FONT SIZE=2 FACE="Arial">The System is a Protein attached to a small Functionalized Surface</FONT>
<BR><FONT SIZE=2 FACE="Arial">composed of ~250 positive carboxyl groups. The hole system is about</FONT>
<BR><FONT SIZE=2 FACE="Arial">220,000 atoms. (amber,tip3p)</FONT>
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<P><FONT SIZE=2 FACE="Arial">The big concern is how to deal with a net charge of almost "-250" ?</FONT>
<BR><FONT SIZE=2 FACE="Arial">(guide me DNA guys)</FONT>
<BR><FONT SIZE=2 FACE="Arial">1) Should I add a huge amount Na+ as counter ions ? Randomly ?</FONT>
<BR><FONT SIZE=2 FACE="Arial">2) And what about long-range electrostatics ? PME would be fine, or</FONT>
<BR><FONT SIZE=2 FACE="Arial">should I try Reaction-Field ?</FONT>
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<P><FONT SIZE=2 FACE="Arial">Thanks,</FONT>
<BR><FONT SIZE=2 FACE="Arial">--</FONT>
<BR><FONT SIZE=2 FACE="Arial">Diego Enry B. Gomes</FONT>
<BR><FONT SIZE=2 FACE="Arial">@ Pacific Northwest National Laboratory.</FONT>
<BR><FONT SIZE=2 FACE="Arial">Laboratório de Modelagem e Dinamica Molecular</FONT>
<BR><FONT SIZE=2 FACE="Arial">Universidade Federal do Rio de Janeiro - Brasil.</FONT>
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