Dear Pratik, > > > 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 | xOH1 is the vector from O to H1, (not just the x component) | xOH1 + xOH2 | is normalisation factor as these vectors are not of unit length > ; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 | again | xOH1 X xOH2 | is a normalisation factor as the cross product of the vector from O to H1 with the vector from O to H2 will not be a unit vector. > ; =20 > ; > ; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2)
This is a standard vector identity the modulus of the cross product of two vectors is the product of the moduli times the sine of the angle between them: |V X U| = |V||U|sin(theta) Hope that's helpful Richard > ; | 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. > > > Thanks, > > Pratik Kaku > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
