[gmx-users] Oscillating Electrical Field

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 23 10:52:11 CET 2009

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.hall at bioch.ox.ac.uk
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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