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I've recently programmed an animated simulation of the main elements (core planets and Sun) of our solar system: by using the initial coordinates from the JPL (Jet Propulsion Laboratory - NASA) database, and then calculating the combined gravitational perturbations and the relativistic effects from the Sun.

However I would now like to calculate the trajectories for both Voyager 1 & 2, and then map them onto my simulation. I can easily replicate the gravitational calculations used for the planets and the Sun, but I'm afraid I'm struggling to find, or figure out, how to replicate the various thrusts manoeuvres used throughout the voyagers' mission.

Any thoughts, insights or advice would be much appreciated, thank-you?

Current method: Calculate voyagers trajectory purely using gravitational effects and initial position/velocity, and then compare calculated data with JPL data, taking into account error, to calculate any unnatural changes in velocity (i.e. thrusts). The difficulty with this method however, is trying to derive meaningful data from the error comparison, any help here would also be much appreciated.

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A different, but somewhat related question Unravelling Cassini's “ball of yarn” orbit around Saturn, tabulation of propulsive maneuvers? has an answer you may find helpful.

This answer to the question "How to calculate the planets and moons beyond Newtons's gravitational force?" might be helpful as well, though it sounds like you've got the integration under control.

Also be warned that the reconstructed parts of historical trajectories in Horizons can have numerical artifacts that look like propulsive maneuvers but aren't. See Is this what station keeping maneuvers look like, or just glitches in data? (SOHO/Horizons)

Also see Why do the LRO's orbital elements appear to constantly oscillate - except recently?

Looking into the data available in JPL's Horizons for Voyager 1 and 2, you will see that these may not precicely represent what you might first think that they do. Patched conics are an approximation and there may be very large glitches when "spheres of influence" boundaries are crossed that are not real, or they may have been numerically smoothed-over afterward, making them "patched and smoothed conics" ;-) See also How to best patch my conics? and the several helpful answers there.

JPL Horizons for Voyager 1

Revised: Jan 21, 2015   Voyager 1 Spacecraft (interplanetary) / (Sun)     -31
                         http://www.jpl.nasa.gov/missions/voyager-1/

 BACKGROUND
   See the web-page above for extensive information on the Voyager Mission.

 SPACECRAFT TRAJECTORY:
   This trajectory is composed of two merged sections:

     #1) 1977-Sep-5 to 1986-Jan-1:
          A patched conic mission-design type trajectory in which the conics 
          were constructed to approximately match specific events (such 
          satellite encounters), providing a rough accuracy. 

     #2) 1986-Jan-1 to 2031-Jan-1 (pfile_a54206u)
          Time-extended trajectory provided by Voyager Navigation

Revised: Jan 21, 2015   Voyager 2 Spacecraft (interplanetary) / (Sun)     -32
                         http://www.jpl.nasa.gov/missions/voyager-2/

 BACKGROUND
   See the web-page above for extensive information on the Voyager Mission.

 SPACECRAFT TRAJECTORY:
   This trajectory is composed of two merged sections:

     #1) 1977-Aug-20 to 1989-Oct-01:
          A patched conic mission-design type trajectory in which the conics 
          were constructed to approximately match specific events (such 
          satellite encounters), providing a rough accuracy. 

     #2) 1989-Oct-01 to 2031-Jan-01 (pfile_m05016u_V0.2):
          Time extended trajectory from Voyager Navigation
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    $\begingroup$ Thanks so much for the help, this is extremely useful :). $\endgroup$ – Tarius Mar 3 '18 at 23:16
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You're going to have to go digging, but the information you're looking for can be found in the Planetary Data System, which has files with spacecraft events including maneuvers.

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