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There is an option called "Toggle Running Silent" - it is suggested that this functionality is used during the alpha 1 mission Predator and Prey as it dramatically reduces your ship's signature and prevents the mercenary in that mission from being able to spot you while you engage a couple of smaller ships some distance away from him.

While "Running Silent" is enabled, my the temperature of my ship continually increases and there doesn't appear to be anything I can do about it.

What happens to my ship if I overheat it? Are there any methods of managing the heat gained while running silent?

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    "Silent Running" can also be used to avoid being scanned when you dock. Useful if you're wanted by the authorities at that station or if you're carrying stolen or illegal cargo. – Cmdr Freiheit Dec 8 '14 at 4:26
  • @CmdrFreiheit Are you sure about that? I've tried docking silent before, and with a lot of stuff shut down to reduce the heat signature, and still gotten scanned. – Iszi Sep 15 '15 at 14:39
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    @Iszi: Silent running helps with avoiding being scanned by authorities, but getting past them and into the station before they scan you is more important. I've done plenty of docking when wanted in a system now, and I never bother with silent running; I boost as much as I can, and use vertical/lateral thrusters to get lined up as I'm boosting in. – Cmdr Freiheit Sep 15 '15 at 22:55
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Once your ship temperature gets to 150%, you start taking an increasing amount of hull damage until your ship explodes.

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Reducing Heat Generation

There doesn't appear to be a method of preventing heat from building up while running silent, although toggling the power state of the various ship modules in your ship and the amount of throttle provided to the engines will affect how quickly the heat builds up.

For example, running through the overheat process with various systems on I found:

  • Powered: Engines, Life Support, Power Distribution, Sensor Suite, Engine throttle at 55%: 3 minutes 4 seconds
  • Powered: Engines, Life Support, Power Distribution, Sensor Suite, Engine throttle at 141%: 1 minute 54 seconds
  • Powered: Engines, Life Support, Power Distribution, Sensor Suite, Engine throttle at 159%: 1 minute 46 seconds
  • Powered: Engines, Life Support only, Engine throttle at 159%: 2 minutes 13 seconds

All tests were performed by starting from 0% total heat generated, toggling on all of the systems I was using for the test and running silent mode at the same time to provide the most accurate numbers. All tests used the default power distribution.

To confirm whether the amount of power sent to the engine through power distribution mattered I did one more run with identical parameters to above but with all power diverted to the weapons (which were disabled on the modules screen) and the shields (which were also disabled on the modules screen). This capped the maximum throttle percentage at 99%;

  • Powered: Engines, Life Support, Power Distribution, Sensor Suite, Engine throttle at 99%: 1 minute 46 seconds

I found this odd, but then considered that perhaps (a little illogically), the heat generated was tied to the actual throttle percentage rather than what is displayed on the screen. Since with no power going to the engines, 99% on screen is in fact 100%, while with two blocks of power going to the engine 159% on screen was in fact 100%, that perhaps the best solution to getting the best efficiency out of running silent would be to divert as much power as possible to the engines. Since shields are disabled while running silent, I diverted 4 blocks of power to the engines and 2 blocks of power to the weapons (which were in fact disabled on the modules screen), and then attempted to get the throttle to 99% on screen while running with the same configuration as before:

  • Powered: Engines, Life Support, Power Distribution, Sensor Suite, Engine throttle at 108%: 2 minutes 38 seconds

Managing Heat Generation

It is possible to purchase a "heat sink launcher", which requires heat sinks as a form of ammunition but allows you to eject heat sinks to reduce your current heat level. Additionally, it is possible to use the heat sink launcher while in silent running mode.

Conclusion

I concluded from the above testing that the best way to get maximum time out of running silent without having to stop to cool down would be:

  • Full power to the engines in power distribution
  • Low throttle % - something like 50-75
  • Turn off shields

This should provide you about three minutes (ish) of time in running silent without having to stop to cooldown.

Another thing I did notice during testing, the engines generate a lot of heat - so much in fact, that even with all of the other systems off and the ship at a stand still, if the heat percentage is above 0% when you active silent running, the heat percentage will climb by itself, regardless of whether the ship is moving or not.

  • I've read that if you equip the "mirrored" military bulkheads, they're very resistant to thermal damage and you can go quite a bit above 150% before taking damage. – Cmdr Freiheit Jan 23 '15 at 22:08
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    Since the Wings update, the temperature readouts are now different. You may want to edit the answer, as 150% for taking damage is no longer accurate. – Shaamaan Mar 25 '15 at 10:44
  • +1 to @Shaamaan - Heat damage starts to accumulate around 100% now. I most certainly wouldn't want my ship to reach 150% these days. – Iszi Feb 8 '17 at 17:52
  • Also, different ships have drastically different heat characteristics—for example, the Diamondback Scout runs very cool. – SilverWolf - Reinstate Monica Feb 3 '18 at 1:23
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I would like to add one crucial thing missing to kalina's answer:

There's a "heat sink launcher" module (which can be placed on any utility hardpoint). Such a module, when used, will rapidly cool your ship down.

It can be used while silent-running but be aware, that it requires "heat sinks" (as ammunition) - therefore it's not possible to use it indefinitely. You CAN, however, outfit more than one launcher, if you so desire.

It is also worth adding that a higher grade power plant can increase heat efficiency, letting one survive for longer when silent running / travelling near stars.

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