> I am not able to understand meaning of "points of lowest/highest
> electrostatic potential" where counter charge is placed in
> http://ambermd.org/tutorials/basic/tutorial1/section2.htm
Highest/lowest is in the context of a set of points in grid
shape wrapped around the solute, maybe 10A wide (I forget
the exact dimension).
> 1) so does counterion is placed at farthest position always?
It turns out that since atomic charge is both negative and
positive within the solute, even with a net charge for the
whole solute, there can be local minima close in.
> 2) "Calculating grid charges" is displayed when addions is
> used..somebody please explain why this is required... or
> source from where I can know how calculations being done or
> atleast philosophical concept....
See above - the leap code is also available.
The initial points for the ions are somewhat arbitrary, as is
water placement; it is up to the user to equilibrate the ions
along with the water.
Bill
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Received on Fri Jul 09 2010 - 10:30:04 PDT
