[AMBER] counterions placings

From: Jio M <jiomm.yahoo.com>
Date: Thu, 8 Jul 2010 23:46:48 -0700 (PDT)

Dear AMBER users,

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

Actually confusion is V inversely related to r and if net system charge is +q then only at infinite V will be minimum that is zero.....(I read it at http://farside.ph.utexas.edu/teaching/316/lectures/node35.html)

1) so does counterion is placed at farthest position always? but it seems some problem in my understanding of the concept

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....

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Received on Fri Jul 09 2010 - 00:00:04 PDT
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