From: Axel Kohlmeyer (
Date: Sun Jan 01 2012 - 11:11:24 CST

On Sun, 2012-01-01 at 13:27 +0330, sarah k wrote:
> Dear all,
> I need to simulate a box of water-protein in the presence of
> electromagnetic field. Is it possible to run such MD simulation by
> NAMD? Is it possible with current simulation packages? I would thank
> any hint or help.

yes, in principle that is possible, but it will
require some programming or scripting. a big question
is to what level of detail and accuracy (and what
strength of magnetic field) do you want to do the
study. classical MD just uses classical mechanics,
so all you need to do is to compute the force
vector on a moving charge in the magnetic field.
in the simplest case of a homogeneous, strong field
it would simply be an additional force term that
is orthogonal to the field and velocity vector
and scaled by the velocity and magnitude of the field.


> Best regards,
> Fatemeh Keshavarz

Dr. Axel Kohlmeyer
College of Science and Technology,
Institute for Computational Molecular Science,
Temple University, Philadelphia PA, USA.