RE: [gmx-users] TIP5P calculating the dummy positions
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)) 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 listgmx-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
RE: [gmx-users] TIP5P calculating the dummy positions
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 listgmx-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
Re: [gmx-users] TIP5P calculating the dummy positions
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 listgmx-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 listgmx-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
