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<TITLE>The meaning of rlist, rvdm and rcolumn</TITLE>
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<P><FONT SIZE=2 FACE="Arial">Dear all:</FONT>
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<P><FONT SIZE=2 FACE="Arial">I searched this mailing list but become even more confused. Who can help to clarify the exact meaning of these parameters. </FONT></P>
<P><FONT SIZE=2 FACE="Arial">I copied this from this list, which said what I want and seemed got no answer.</FONT>
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<P><FONT SIZE=2 FACE="Arial">Thanks.</FONT>
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<P><FONT SIZE=2 FACE="Arial">Li, Dawei</FONT>
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<P><FONT SIZE=2 FACE="Arial">*******************************************************</FONT>
<BR><FONT SIZE=2 FACE="Arial">dear all,</FONT>
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<P><FONT SIZE=2 FACE="Arial">I do MD simulations using a cutoff for</FONT>
<BR><FONT SIZE=2 FACE="Arial">both VdW and Coulomb interactions.</FONT>
<BR><FONT SIZE=2 FACE="Arial">I am rather confused about the</FONT>
<BR><FONT SIZE=2 FACE="Arial">parameters used in the input file.</FONT>
<BR><FONT SIZE=2 FACE="Arial">(rlist, rvdw, rcoulomb)</FONT>
<BR><FONT SIZE=2 FACE="Arial">I searched this mailing list</FONT>
<BR><FONT SIZE=2 FACE="Arial">for clarification, but I found two</FONT>
<BR><FONT SIZE=2 FACE="Arial">statements that appear to contradict</FONT>
<BR><FONT SIZE=2 FACE="Arial">each other (just as the documentation</FONT>
<BR><FONT SIZE=2 FACE="Arial">does by the way). The two mails are: </FONT>
<BR><A HREF="http://www.gromacs.org/pipermail/gmx-users/2002-June/028443.html"><U><FONT COLOR="#0000FF" SIZE=2 FACE="Arial">http://www.gromacs.org/pipermail/gmx-users/2002-June/028443.html</FONT></U></A>
<BR><A HREF="http://www.gromacs.org/pipermail/gmx-users/2003-January/030507.html"><U><FONT COLOR="#0000FF" SIZE=2 FACE="Arial">http://www.gromacs.org/pipermail/gmx-users/2003-January/030507.html</FONT></U></A>
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<P><FONT SIZE=2 FACE="Arial">Normally I would assume that if one uses</FONT>
<BR><FONT SIZE=2 FACE="Arial">a neighbour list there are (at least) two cutoffs:</FONT>
<BR><FONT SIZE=2 FACE="Arial">One for a sphere around each atom with ALL</FONT>
<BR><FONT SIZE=2 FACE="Arial">(and only) the atoms in this sphere considered when</FONT>
<BR><FONT SIZE=2 FACE="Arial">calculating the energy and the forces on</FONT>
<BR><FONT SIZE=2 FACE="Arial">the primary atom at EACH time step (rvdw,</FONT>
<BR><FONT SIZE=2 FACE="Arial">rcoulomb ?).</FONT>
<BR><FONT SIZE=2 FACE="Arial">A second (larger) cutoff that is used when</FONT>
<BR><FONT SIZE=2 FACE="Arial">calculating the neighbour-list at intervals</FONT>
<BR><FONT SIZE=2 FACE="Arial">of each 10 (or so) time steps (rlist ?)</FONT>
<BR><FONT SIZE=2 FACE="Arial">were of course rlist > rvdw and rcoulomb.</FONT>
<BR><FONT SIZE=2 FACE="Arial">(it is also possible to have the program</FONT>
<BR><FONT SIZE=2 FACE="Arial">calculate this parameter nstlist automatically</FONT>
<BR><FONT SIZE=2 FACE="Arial">thereby optimizing the performance, this is</FONT>
<BR><FONT SIZE=2 FACE="Arial">not implemented in Gromacs, is it ?)</FONT>
<BR><FONT SIZE=2 FACE="Arial">If one uses a switched potential there</FONT>
<BR><FONT SIZE=2 FACE="Arial">is a third cutoff (the onset of the switching</FONT>
<BR><FONT SIZE=2 FACE="Arial">function) that would be shorter than</FONT>
<BR><FONT SIZE=2 FACE="Arial">rvdw and rcoulomb.</FONT>
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<P><FONT SIZE=2 FACE="Arial">this implies: rlist > rvdw,rcoulomb > r*_switch</FONT>
<BR><FONT SIZE=2 FACE="Arial">... in contrast to (part of) the docu, and the</FONT>
<BR><FONT SIZE=2 FACE="Arial">errormsg given by the code, and to one of the</FONT>
<BR><FONT SIZE=2 FACE="Arial">messages cited above.(the message of Anton</FONT>
<BR><FONT SIZE=2 FACE="Arial">Feenstra reminds me rather of another concept,</FONT>
<BR><FONT SIZE=2 FACE="Arial">namely the multiple timestep algoritm which, if </FONT>
<BR><FONT SIZE=2 FACE="Arial">I am not mistaken, is not implemented</FONT>
<BR><FONT SIZE=2 FACE="Arial">in Gromacs)</FONT>
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