VMD-L Mailing List

From: sarah k (dailycolors_at_gmail.com)
Date: Mon Jan 02 2012 - 06:22:10 CST

Dear Axel Kohlmeyer

 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.

 I'm going to study the effect of low frequency electromagnetic fields
(30-100 Hz) at several temperatures. Actually, It's a part of my MSc.
thesis and I want to perform both experimental and simulation studies. The
results will be compared to each other so I need high precision and
accuracy and reproducibility of results.

> 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.
>
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science and Technology,
> Institute for Computational Molecular Science,
> Temple University, Philadelphia PA, USA.
>
>

I know that simulation is not like in vitro studies but can I hope that if
electric field be applied to the system, magnetic field will be
consequently produced? The proteins have polar residues and as a logical
result external electrical field will make the electrical dipole momentum
rotate and respectively magnetic field will be formed. So is namd trustable
for my purpose if I only apply electric field? Thanks.

Regards,
Fatemeh