Dear Users, I am trying to obtain the dipole moment of a 40 amino acid residue peptide using g_dipoles. I am getting a huge number (about 700 Debye). I expect it to be around 150 Debye (based on other studies). To make sure it I extracted a shapshot of the structure and obtained the dipolemoment using the following command:
g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg -n prot_dip.ndx I am giving the last few lines of the output below: Dipole moment (Debye) --------------------- Average = 516.7213 Std. Dev. = 0.0000 Error = 0.0000 The following averages for the complete trajectory have been calculated: Total < M_x > = -54.3459 Debye Total < M_y > = 12.8373 Debye Total < M_z > = 513.695 Debye Total < M_x^2 > = 2953.47 Debye^2 Total < M_y^2 > = 164.796 Debye^2 Total < M_z^2 > = 263883 Debye^2 Total < |M|^2 > = 267001 Debye^2 Total < |M| >^2 = 267001 Debye^2 < |M|^2 > - < |M| >^2 = 0 Debye^2 Finite system Kirkwood g factor G_k = 0 Infinite system Kirkwood g factor g_k = 0 Epsilon = 1 The same structure (i.e., what i have used in the above command) if I open and check for the dipole moment using YASARA suite of program it is showing as 173 Debye. Which is reasonable. Am I making any mistake while obtaining the dipole moment using g_dipoles or I am looking at the wrong file ?? Thanks. Ram.
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