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<p class=MsoNormal>Hi there,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>For the past few months, I’ve been adding a charge equilibration
model to GROMACS (to be specific, QTPIE – a refinement of QEq). For
the model to work properly, each atom must “see” each other atom in
the electrostatic interaction (it is a screened Coulomb interaction). This
is easy enough to do with pbc = no; I just set all the cutoffs to zero, and add
a new neighbor-list that includes excluded atom pairs.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Now I would like to run the simulation with PBC turned on,
which means either implementing Ewald summation or using cutoffs for the
electrostatic interaction. When cutoffs are turned on (with or without
PBC), the model goes haywire even with very long cutoff lengths. I haven’t
implemented Ewald summation for the screened Coulomb interaction, and I’m
not sure if it’s worth the effort if an easier fix is possible.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>As a quick fix, I changed the simple neighbor-searching code
to set rcut = 1000000 when QTPIE is turned on (normally forbidden under normal
GROMACS run conditions). This brings the charges back to normal in a
periodic box, plus I now get complete uniformity of the charges in crystalline systems
(e.g. in FCC NaCl, the charges on the Na atoms are all the same). I think
this works because simple neighbor-searching with an infinite cutoff length has
the effect of counting every neighbor once while still following the minimum
image convention. I have verified this by looping through the atoms in
the neighbor list, and counting the number of interactions as well as printing the
shifted interatomic distances for a water box. I consistently count
N*(N-1) interactions for a N-atom box, and the shifted interatomic distances
are consistently under half of the box diagonal.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am worried about the other possible consequences of my change;
will this adversely affect the molecular dynamics or create artifacts in some
unexpected way? I am aware that this will lead to situations where a
solvent molecule may see both sides of a larger solute, but I can accept those
relatively small effects. My main goal is to run NPT dynamics on a QTPIE water
model and verify physical properties like density, dielectric constant, etc.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks a lot for your help!<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Lee-Ping<o:p></o:p></p>
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