[gmx-users] Oscillating Electrical Field
Benjamin Hall
benjamin.hall at bioch.ox.ac.uk
Mon Feb 16 16:22:07 CET 2009
Hi
I'm trying to create an oscillating electrical field in my simulation,
and I was hoping that someone who had successfully done this in the
past could please offer some advice on the choice of parameters in my
mdp. Eventually, I would like to create a system with oscillating
fields across both x and y, pi/2 radians out of phase in order to
cause a body in my simulation to rotate by aligning its charge
distribution to the field. At the moment, I would just like to find
out a couple of things about exactly which parameters to use.
I've looked at the source code from src/mdlib/sim_util.c and tried out
a few combinations, and as far as I can see you need to enter
parameters for the x axis (as an example) in both E_x and E_xt,
representing the maximum field strength. E_x values are chosen as
described in the manual. E_xt takes three values- the first value has
to be 1 (to generate an oscillating field), the second value a number
related to the frequency of the wave, and the third value a measure of
phase so that you can vary the starting values of the field. Other
values are ignored.
My first question is have I interpreted these values correctly? Also,
the code refers to t, which I assume to be the time. What is the units
of t, and does to cosine function expect radians or degrees? Also,
there seems to be an optional term which causes the waves to decrease
exponentially over time-
Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));
can I turn this off or ignore it if I want to specify a phase?
Many thanks in advance
Ben
************************************************************************
Benjamin A. Hall
Structural Bioinformatics & Computational Biochemistry Unit / OCISB
University of Oxford
http://sbcb.bioch.ox.ac.uk/hall.php
+44 (0)1865 613304
benjamin.hall at bioch.ox.ac.uk
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