Benjamin Hall wrote:
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?
I think your guesses are mostly correct. But what's more, mdrun will
output an xvg file containing the applied field such that you can use
trial and error.
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.h...@bioch.ox.ac.uk
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