[gmx-users] Problem in calculating static dielectric constant of Lysozymes
Suman Das
sumandas212 at gmail.com
Tue Oct 31 20:57:00 CET 2017
Dear Gromacs Users,
I am trying to calculate static dielectric constant of Lysozymes using
gromacs version 4.6.7. I tried to follow the protocol used earlier by van
Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014). I used PME for the
electrostatic interaction. First, I converted the trajectory of protein by
using the command 'trjconv -f traj.xtc -o protein.xtc -pbc whole -e
1000.0". Then I removed the translational and rotational motion of the
protein w.r.t the C-alpha atom by the following command "trjconv -f
protein.xtc -o protein_fit.xtc -fit rot+trans". I choose C-alpha for the
least square fit. And finally g_dipoles command to calculate the dielectric
constant "g_dipoles -f protein_fit.xtc -o Mtot.xvg -eps epsilon.xvg -a
aver.xvg -d dipdist.xvg -c dipcorr.xvg". However, the dielectric constant
value (1.04) that I am getting is very less compared to the actual
dielectric constant (30).
Dipole moment (Debye)
---------------------
Average = 172.7138 Std. Dev. = 7.4113 Error = 0.0524
The following averages for the complete trajectory have been calculated:
Total < M_x > = 38.9789 Debye
Total < M_y > = 54.2911 Debye
Total < M_z > = -158.896 Debye
Total < M_x^2 > = 1575.16 Debye^2
Total < M_y^2 > = 3006.62 Debye^2
Total < M_z^2 > = 25303.2 Debye^2
Total < |M|^2 > = 29885 Debye^2
Total |< M >|^2 = 29714.9 Debye^2
< |M|^2 > - |< M >|^2 = 170.091 Debye^2
Finite system Kirkwood g factor G_k = 0.00570201
Infinite system Kirkwood g factor g_k = 0.00561463
Epsilon = 1.04819
Could you help me to find out what probably went wrong with the calculation?
Thanks,
Suman
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