Dear Pratik, > Dear Richard, > > First of all i really appreciate the help. I 've figured out the cross > product part of the equations, but the |A+B| part i still have figured > it out. > > I've been trying to crack this bit but I still can't do it. > > 0.07 * cos (109.47/2) / | xOH1 + xOH2 | -> this bit is what i dont get > below is what i've done > > based on what you said xOH1 is the distance of O to H (bond lenght of > OH being 0.09572, x-axis 0.07595, y-axis 0.058588) and the bond angel > of HOH=104.52 > > putiing it into the equation: > > 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ---(expansion)---> > 0.07*cos (109.47/2) /(2*|OH|*cos(HOH)) this expansion is not quite right for the modulus of the sum of two vectors, | xOH1 + xOH2 | = sqrt(| xOH1 |^2 +| xOH2 |^2 +2 xOH1 [dot] xOH2 ) | xOH1 + xOH2 | = |xOH1|*sqrt(2+2*cos(HOH))
if you run that calculation through you should get the right result. Regards, Richard > > plugging in the numbers: > > 0.07*cos (109.47/2) /(2*0.09572*cos(104.52)) = 0.040440/0.0479974 = > -0.842546 (the answer i get) > > -0.842546 is the answer i get how ever the answer i should be getting > is -0.344908 . I've tried to look for solutions to this but i still > don't understand it. > It would be very helpful if you could show me where i have gone wrong. > > > Thanks, > Pratik Kaku > > > > > Subject: Re: [gmx-users] TIP5P calculating the dummy positions > > From: richard.broadben...@imperial.ac.uk > > To: gmx-users@gromacs.org > > Date: Fri, 21 Oct 2011 11:40:04 +0100 > > > > 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 > -- 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
