<br><br><div class="gmail_quote">On 10 February 2012 09:41, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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On 11/02/2012 1:19 AM, Elisabeth wrote:
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<blockquote type="cite">Hello all,<br>
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Does the shift function use group based truncation? <br>
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See the discussion of charge groups in manual section 3.4.2.</div>
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Thanks Mark. <br>
<br>
-1- First of all if I am right charge groups in gromacs
language in identical to "group based truncations"?</div>
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Using charge groups as the indivisible entity upon which neighbour
list construction is based is using "group based truncations". The
usual alternative is using atoms as the, well, *atomic* unit. The
former can be equivalent to the latter if there's one atom per
charge group.<div class="im"><br>
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Manual 342: "This reduces the cut-off effects from the
charge-charge level to the dipole-dipole level, which decay
much faster"<br>
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2- I am not able to realize why we go from charge-charge the
dipole-dipole changes?<br>
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Charge groups are constructed to have neutral charge (or integer
charge where necessary). To first order, the difference between any
such group being in the neighbour list of another such group or not
(according to the cut-off radius) is equivalent to a point dipole
being in the cut-off sphere or not. Charge groups with arbitrary
charge (or partially-charged atoms, when using atom-based
truncation) do not have this quality, and the distance at which a
charge-charge interaction is significant is much larger than that of
a dipole-dipole.<div class="im"><br>
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<blockquote type="cite"> In the manual I see: by using
shifted forces there is no need for charge groups
(=group based?!) in the neighbor list? <br>
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Can anyone shed some light on calculation of shifted
forces? <br>
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What's not clear from the above and 4.1.5?<br>
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3- I understand that use of shift makes the potentials have
continuous derivatives at cutoffs but that how this makes use
of charge groups unnecessary, I dont see!<br>
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Remember that the neighbour list is constructed to permit the
computation of a finite number of interactions with the central
atom/group. You want to stop computing them when they're close
enough to zero that you don't care. If they actually go to zero,
then you don't care. If they decay as 1/r (charge-charge) then at
typical r_c values you should care. If they decay as 1/r^2
(dipole-dipole, IIRC) then at typical r_c values things are OK.<br>
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If the value of the force is non-zero at the cut-off, then there is
an interaction at that distance and not one just past that distance.
This generates artefacts that are serious for non-zero charges at
the kinds of cut-off distances for which force fields are
parametrized, but much less serious if computed over neutral charge
groups.<br>
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If the value of the force is zero at the cut-off (i.e. shift
potential), then no atom or charge group has any interaction with
the central group/atom at that distance, </div></blockquote><div><br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
so you don't need to care
about whether the truncation is based on atoms or groups. You do
have to care about the effect of the modified Coulomb potential,
however.<div class="im"><br>
Hello Mark,<br></div></div></blockquote><div><br>I read over your answer several times. I am still unclear about " modified Coulomb potential". In the manual modified Coulomb potential refers to shift/switch functions, as I realized. so when the force is zero at r_c and it doesnt matter whether truncation is based on atoms or groups, why effect of modified coulomb potential is important?<br>
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