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Dear Richard,<BR>
<BR>
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.<BR>
<BR>
I've been trying to crack this bit but I still can't do it.<BR>
<BR>
<STRONG>0.07 * cos (109.47/2) / | xOH1 + xOH2 | </STRONG>-> this bit is what i dont get below is what i've done<BR>
<BR>
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<BR>
<BR>
putiing it into the equation:<BR>
<BR>
0.07 * cos (109.47/2) / | xOH1 + xOH2 | ---(expansion)---> 0.07*cos (109.47/2) /(2*|OH|*cos(HOH))<BR>
<BR>
plugging in the numbers:<BR>
<BR>
0.07*cos (109.47/2) /(2*0.09572*cos(104.52)) = 0.040440/0.0479974 = -0.842546 (the answer i get)<BR>
<BR>
-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.<BR>
It would be very helpful if you could show me where i have gone wrong.<BR>
<BR>
<BR>
Thanks,<BR>
Pratik Kaku<BR>
<BR>
<BR> <BR>
<DIV>
> Subject: Re: [gmx-users] TIP5P calculating the dummy positions<BR>> From: richard.broadbent09@imperial.ac.uk<BR>> To: gmx-users@gromacs.org<BR>> Date: Fri, 21 Oct 2011 11:40:04 +0100<BR>> <BR>> Dear Pratik,<BR>> <BR>> > <BR>> > <BR>> > I am trying to create the tip6p itp file. In order to do that, since<BR>> > it is an overlap of the tip4p and tip5p model (visually)<BR>> > I am trying to understand the a, b, and c values for the position of<BR>> > the dummy charge in the tip5p models.<BR>> > <BR>> > Below is the part of the script that is of my concern.<BR>> > _________________________________________________________<BR>> > [ dummies3 ]<BR>> > ; The position of the dummy is computed as follows:<BR>> > ;<BR>> > ; The distance from OW to L is 0.07 nm, the geometry is tetrahedral<BR>> > ; (109.47 deg)<BR>> > ; Therefore, a = b = 0.07 * cos (109.47/2) / | xOH1 + xOH2 |<BR>> xOH1 is the vector from O to H1, (not just the x component)<BR>> | xOH1 + xOH2 | is normalisation factor as these vectors are not of unit<BR>> length<BR>> > ; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 |<BR>> again | xOH1 X xOH2 | is a normalisation factor as the cross product of<BR>> the vector from O to H1 with the vector from O to H2 will not be a unit<BR>> vector.<BR>> > ; =20<BR>> > ;<BR>> > ; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2)<BR>> <BR>> This is a standard vector identity the modulus of the cross product of<BR>> two vectors is the product of the moduli times the sine of the angle<BR>> between them:<BR>> <BR>> |V X U| = |V||U|sin(theta)<BR>> <BR>> Hope that's helpful<BR>> <BR>> Richard<BR>> <BR>> > ; | xOH1 + xOH2 | = 2 | xOH1 | cos (H1-O-H2)<BR>> > ; Dummy pos x4 = x1 + a*x21 + b*x31 + c*(x21 X x31)<BR>> > ; Dummy from funct a b c<BR>> > 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493<BR>> > 5 1 2 3 4 -0.344908 -0.344908 6.4437903493<BR>> > _______________________________________________________<BR>> > <BR>> > I do understand everything except the bolded bit.<BR>> > <BR>> > so far i have understood that |xOH1| is the magnitude of OH on the<BR>> > x-axis, but putting those values in i don't the the correct a, b, c.<BR>> > I'm not good in vectors and i have had a look at the gromacs manual<BR>> > (the 3out model ni figure 4.16).<BR>> > <BR>> > I don't know where i am going wrong. <BR>> > <BR>> > I would appreciate the help thanks.<BR>> > <BR>> > <BR>> > Thanks,<BR>> > <BR>> > Pratik Kaku<BR>> > <BR>> > <BR>> > -- <BR>> > gmx-users mailing list gmx-users@gromacs.org<BR>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> > Please don't post (un)subscribe requests to the list. Use the <BR>> > www interface or send it to gmx-users-request@gromacs.org.<BR>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR>> <BR>> <BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR></DIV> </div></body>
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