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On 10/12/2010 06:49 PM, Lee-Ping Wang wrote:
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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.</p>
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<br>
Since we'd be interested in that, I would appreciate if you can keep
us informed of your progress.<br>
<br>
<blockquote cite="mid:006e01cb6a2d$7b63c600$722b5200$@edu"
type="cite">
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<p class="MsoNormal"><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.</p>
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<br>
If I recall correctly, the screened Coulomb here means the overlap
integral between s-type Slater functions. This interaction behave as
a normal coulomb at large distances, so that coudl explain the
issues with increasing the cut-off. But an Ewald expression will be
difficult as well, since the all pairs-wise interactions are
required to compute the charge flow parameters. I have so far only
seen it applied to molecules. For non bonded system like a box of
water, a direct charge flow between atoms far apart is unlikely
though. Could one not simply scale also the charge transfer
variables to zero with distance as well?<br>
<blockquote cite="mid:006e01cb6a2d$7b63c600$722b5200$@edu"
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<p class="MsoNormal"><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.<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? </p>
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You will get the ordinary artefacts caused by cutoff, like ordering
etc.<br>
<o:p></o:p>
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