Dear All I want to calculate instantaneous dipole moment of a water molecule(from liquid water) in gromacs.I had gone through the archives of the forum but couldn't found much.
I used command g_dipoles with following extension g_dipoles -f 293.trr -s 293.tpr -n atoms.ndx -o Mtot.xvg -mu -1 atoms.ndx contains three atoms of a water molecule. which gave the output as Dipole moment (Debye) --------------------- Average = 2.2740 Std. Dev. = 0.0007 Error = 0.0000 The following averages for the complete trajectory have been calculated: Total < M_x > = -0.00546922 Debye Total < M_y > = 0.0192573 Debye Total < M_z > = -0.0446763 Debye Total < M_x^2 > = 1.68877 Debye^2 Total < M_y^2 > = 1.71468 Debye^2 Total < M_z^2 > = 1.76741 Debye^2 Total < |M|^2 > = 5.17086 Debye^2 Total < |M| >^2 = 0.00239673 Debye^2 < |M|^2 > - < |M| >^2 = 5.16846 Debye^2 Finite system Kirkwood g factor G_k = 0.999537 Infinite system Kirkwood g factor g_k = 0.978649 Epsilon = 1.06689 I am convinced with the value in comparison to that reported in literature. But when I plot the Mtot.xvg I found the fluctuations in dipole from -2.5 to 2.5 D. Is it reasonable to have this kind of behaviour or is it due to change in the direction of dipole vector. I need instantaneous fluctuations to calculate dipole correlation function. Further to calculate dipole moment of water I believe I should use Dflexible in mdp file,for without fluctuations the dipole for rigid water molecule must not change .But It has been strongly demotivated in previous discussions.Please help me in this regard. -- DeepaK Ojha School Of Chemistry "Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live" -- 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
