[gmx-users] (no subject)
demon_lord_pratik at hotmail.com
Fri Oct 21 11:52:48 CEST 2011
To whomsoever it may concern,
I am trying to create the tip6p itp file. In order to do that, since it is an overlap of the tip4p and tip5p model (visually)
I am trying to understand the a, b, and c values for the position of the dummy charge in the tip5p models.
Below is the part of the script that is of my concern.
[ dummies3 ]
; The position of the dummy is computed as follows:
; The distance from OW to L is 0.07 nm, the geometry is tetrahedral
; (109.47 deg)
; Therefore, a = b = 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2)
; | xOH1 + xOH2 | = 2 | xOH1 | cos (H1-O-H2)
; Dummy pos x4 = x1 + a*x21 + b*x31 + c*(x21 X x31)
; Dummy from funct a b c
4 1 2 3 4 -0.344908 -0.344908 -6.4437903493
5 1 2 3 4 -0.344908 -0.344908 6.4437903493
I do understand everything except the bolded bit.
so far i have understood that |xOH1| is the magnitude of OH on the x-axis, but putting those values in i don't the the correct a, b, c.
I'm not good in vectors and i have had a look at the gromacs manual (the 3out model ni figure 4.16).
I don't know where i am going wrong.
I would appreciate the help thanks.
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