Electric fields

A pulsed and oscillating electric field can be applied according to:

(1)\[E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]\]

where \(E_0\) is the field strength, the angular frequency \(\omega = 2\pi c/\lambda\), \(t_0\) is the time at of the peak in the field strength and \(\sigma\) is the with of the pulse. Special cases occur when \(\sigma\) = 0 (non-pulsed field) and for \(\omega\) is 0 (static field).

This simulated laser-pulse was applied to simulations of melting ice 146. A pulsed electric field may look ike Fig. 46. In the supporting information of that paper the impact of an applied electric field on a system under periodic boundary conditions is analyzed. It is described that the effective electric field under PBC is larger than the applied field, by a factor depending on the size of the box and the dielectric properties of molecules in the box. For a system with static dielectric properties this factor can be corrected for. But for a system where the dielectric varies over time, for example a membrane protein with a pore that opens and closes during the simulation, this way of applying an electric field is not useful. In such cases one can use the computational electrophysiology protocol described in the next section (sec. Computational Electrophysiology).


Fig. 46 A simulated laser pulse in GROMACS.

Electric fields are applied when the following options are specified in the grompp mdp file. You specify, in order, \(E_0\), \(\omega\), \(t_0\) and \(\sigma\):

electric-field-x = 0.04 0       0     0

yields a static field with \(E_0\) = 0.04 V/nm in the X-direction. In contrast,

electric-field-x = 2.0  150     5     0

yields an oscillating electric field with \(E_0\) = 2 V/nm, \(\omega\) = 150/ps and \(t_0\) = 5 ps. Finally

electric-field-x = 2.0  150     5     1

yields an pulsed-oscillating electric field with \(E_0\) = 2 V/nm, \(\omega\) = 150/ps and \(t_0\) = 5 ps and \(\sigma\) = 1 ps. Read more in ref. 146. Note that the input file format is changed from the undocumented older version. A figure like Fig. 46 may be produced by passing the -field option to gmx mdrun.