Hydra Nemesis 2 Plug and Play Troubleshooting Instructions

Nemesis Installation Troubleshooting Primer Nemesis Tuning Primer
Wideband Installation Boost Control Installation Ignition Installation

The Hydra Nemesis 2 EMS provides almost unlimited possibilities for adjustment of the engine. This is both a blessing and a curse. It is a blessing because it allows almost any engine configuration to be controlled. The curse is that with so many possible adjustments, it takes some understanding of the way an engine works and the way the Hydra Nemesis 2 unit acts out the settings to get the right things to happen under all conditions. This section gives some guidance to help you get your car running like stock with the Hydra Nemesis 2.

Important Information to know before working on any issue

Early versions of the Hydra Nemesis 2.1 were shipped with a ground wire going to the B10 pin on the small blue connector. This was required to allows you to adjust the fuel and timing maps on the fly while the engine is running. If this pin has been pulled out as is suggested once your engine is tuned, you will want to put it back into place to allow you to make any on-the-fly adjustments required. Note that adjustments made to the fuel and spark maps in on-the-fly mode are completely forgotten by the Hydra Nemesis 2.1 and 2.5 versions when you shut the ignition power off unless you explicitly make them permanent by downloading the changes to the Hydra Nemesis unit through the 'Download button on the entry screen of the laptop software. Note that downloading will always stop the engine if it is running. This is normal. Just be aware of it so that you don't try to download while the car is moving. Pull off somewhere safe. Download the changes. Turn ignition power completely off for at least two seconds, and then turn the power back on and resume normal operation. Always upload the changes you just downloaded after you turn the ignition power back on so that you don't get a warning telling you that the laptop software and the unit may not be completely synched up with the same map settings.

Most of the numeric boxes in the program panels have an 'Enter' button next to them which must be pushed in order to have the new value you typed in sent to the Nemesis.

Any changes made to the 2D and 3D maps other than the fuel and spark map do not get sent to the Nemesis while in on-the-fly mode until you press the 'Return' key on your keyboard. So if you are playing around with the idle target map and it seems to do nothing, be sure that you press the return key on the keyboard before you conclude that the Nemesis system is not working properly.

Regardless of which changes seem to take on-the-fly, always save your changes to a new file (so that you have old settings still available to go back and look at or download if your new settings create problems) and do an explicit download of the changes when the car is not moving at the end of your tuning or trouble shooting section.

Engine does not start

The first order of business is to determine why. We assume here that your engine was running before you put the Nemesis plug and play system on it. The first thing to check is if the check engine light comes on when you turn the ignition key to 'ON' before you try to start the engine. If that isn't happening, then you either have no power going to the Nemesis unit or you installed a map that we didn't provide. Check the EFI fuse in the engine bay fuse box. If it is blown replace it. If it continues to blow, then you need to contact us for help. If the fuse remains good but the check engine light fails to come on, turn the ignition key to 'OFF.' Using a voltmeter, check the voltage between the white-yellow wire with the spade connector and chassis ground (if you have the turbo timer option, this wire is connected to the turbo timer relay). There should be around 12 volts here at all times. If not, the Nemesis is not receiving power from the battery. If that checks out, turn the ignition key to 'ON' and check the voltage between the red wire with the two spade connectors and chassis ground. This should also indicate close to 12 volts. If it does not, the Nemesis is not receiving switched power. If you have power on both wires and the check engine light is off, connect the laptop to the Nemesis and download the appropriate base map for your setup into it (one provided by MR Controls, not something that you got from somewhere else). Cycle the ignition power after you finish the download and switch the ignition back to 'ON' to verify that the check engine light comes on. If not, contact us for additional help.

If the check engine light comes on, connect the laptop to the Nemesis, upload the current map and go to the main tuning screen. The RPM reading at the top right corner should be 0 RPM. Attempt to start the engine and watch the RPM reading. If it goes above 0 RPM, then the Nemesis is receiving a distributor trigger signal. If it doesn't, you need to power down the system and check your plug and play box to insure that your jumpers are properly set for the year and type of engine harness you are using. See here for more details.

If the plug and play system is properly set up for your model and year engine harness but you are not getting a distributor signal, then one of two things may be wrong. The first is that it is possible for a distributor to work with the stock ECU but not with the Nemesis. The reason for this is that the Nemesis reads only one of the two cam angle sensors in the distributor. In one instance, we ran into a distributor that had been damaged when a rotor came loose from the shaft while the engine was turning. The rotor took out the G2 sensor (which the Nemesis reads) but left the G1 intact. The stock ECU reads both and can continue to run even if only one works. If you suspect that this may be the case, try another distributor. If all else fails, you may have a bad engine harness or a faulty Nemesis unit or a unit that is not programmed to work with the 3S-GTE distributor triggers. Contact us for help.

If the engine appears to be making no attempt to actually start but the RPM reading shows some activity, disconnect the main ignition wire going to the distributor and hold it about 1/4" from a good engine ground while somebody cranks the engine to determine if there is a spark. If there is a spark, then the problem is likely to be fuel related. If you have just finished removing the stock fuel injector resistor pack, go back and check your modifications to make sure that they were done correctly. If you have a spare injector (of any size), unplug the injector clip from the #1 cylinder injector and plug the spare injector to it. Have someone attempt to start the engine while you hold the injector in your hand. You should hear and feel the injector click on every other revolution of the engine. If not, check your engine harness to determine why the injector pulses are not reaching the injectors. If the injectors are clicking, the fuel pump may not be supplying fuel. If you have a fuel pressure gauge, check your fuel pressure to insure that you have fuel pressure when the engine is cranking. If you do not have a fuel pressure gauge, upload the map from the Nemesis and go to 'Select->Outputs' to get the outputs panel. Click the 'PWM16' button and set the fuel pump 'PRIMER (S)' value to 5 and click the 'enter' button. Then, have someone switch the ignition key from 'OFF' to 'ON' while you are squeezing one of the fuel lines. The primer setting tells the Nemesis to switch on the fuel pump for five seconds to prime the fuel system whenever the ignition is switched on. This should be plenty of tim for you to feel fuel flowing through the fuel hoses. Try it a couple of times. If you don't feel the fuel flowing then there may be a problem with your body harness or your Nemesis. Contact us for help.

If the ignition is sparking and the injectors are pulsing and fuel is flowing, then the engine must be either getting too much or not enough fuel. If it is getting too much fuel, you will usually be able to smell it in the air after one or two attempts to start the engine. If there is no or very little gasoline smell, the engine may not be getting enough fuel to start. Adjustments to the cranking fuel can be made through the 'Select->Control 2->Cranking Enrichment' map in the Nemesis program. If you suspect the cylinders to be flooded with gasoline, push the gas pedal all the way to the floor to prevent the Nemesis from injecting fuel while the car is cranking. This will push air through the engine and quickly evaporate the fuel. Make sure that you have calibrated the TPS properly before doing this, because the Nemesis must know that the throttle is wide open for this clearing procedure to properly work.

Engine reliably starts and then stalls when warm

The most likely reason why the engine should start and almost immediately stall when it is warm is insufficient fuel in the idle portion of the fuel map. The first thing you need to determine to solve this problem is which cells in the fuel map correspond to the idle region of your engine. This can vary depending on the engine configuration. First, ensure that the Nemesis is using the main fuel map and not one of the alternate maps by making sure that the switch on the plug and play box is set to the center position. Go to 'Select->Fuel' to see the main fuel map. Go to 'View->Floating Grid' to open up the large version of the fuel map. Then, click the 'Reset trace' button to set all the cells on the map back to their normal form. Start the engine and let it attempt to idle without applying any fuel. If the engine stalls, then you now have a trace of the cells that the Nemesis consulted while the engine ran in bold. The trace should move from about zero vacuum down to the normal operating vacuum level of the engine (if it doesn't, check the vacuum hose going to the Nemesis to make sure you have it properly connected to the intake manifold). Press the 'Rpm hold' button to allow you to move the cursor down to the region of cells where the engine tried to go to as it approached maximum vacuum. You must press the space bar to switch between adjustment mode and move up and down the rows mode. Also, pressing the '+' button next to the '0.005' at the bottom right of the screen allows the up and down key to make bigger fuel adjustments. Add about 10% more fuel not just to the cells that were highlighted, but also to the surrounding cells as well. When you are done, click he 'Rpm track' button to put the cursor back in tracking mode and the 'Reset trace' button to clear the map once again. Attempt to start the engine once again. If it continues to stall, repeat the process several more times adding fuel until the engine finally gets to a point where it continues to run after it is started.

Engine starts and idles but blows black smoke or spits soot from the exhaust

This is a classic case of running too rich. The first thing is to make sure that the Nemesis is seeing vacuum in the intake manifold. Look at the main panel of the Nemesis program and make sure that the gauge labeled 'boost (mm Hg/psi)' is showing a reasonable amount of vacuum. Even with the biggest cams you should idle at least at or below 300mm Hg. If not, check the vacuum hose from the Nemesis to your intake manifold to be sure that it is properly connected and not crushed or kinked at any point. Pull the hose out of the Nemesis port and verify that there is a strong vacuum there by covering it with your finger. If you have a strong vacuum but the Nemesis boost gauge does not register any change in vacuum reading when you plug the vacuum hose in, then the MAP sensor in the Nemesis must be faulty. Contact us for help.

If the boost gauge reads properly, go to 'Select->Settings' and click the 'CLOSED LOOP' button. Uncheck the 'ENABLE CLOSED LOOP' box. Wait a few seconds. If the exhaust clears up, then you either have a bad oxygen sensor which is driving the Nemesis to richen up the fuel mixture too much or you have at least one cylinder which is misfiring and causing the fuel mixture to appear lean because of all the extra oxygen that the missing cylinder is pumping into the exhaust system. To determine if one of your cylinder is misfiring, pull off each spark plug wire at the spark plug end and pull it away from the plug terminal. If the speed and note of the engine does not change when you pull off the spark plug wire and push it back in, then that cylinder is not firing. Test each cylinder this way to see if any one is misfiring. If you find the misfire, fix it before you re-enable closed loop operation. If no cylinders are missing but the rich condition resumes whenever closed loop is enabled, you either have a faulty oxygen sensor or engine harness. Contact us for help.

Go to 'Select->Settings' and click the 'ISC' button. Set 'MAX VACUUM (mmHg) to about 50mm Hg more vacuum than your engine normally produces at idle when it is warm and click 'enter.' This value actually limits the maximum vacuum that the Nemesis uses when the throttle is completely closed. If it is set to less vacuum than the engine produces at idle, then the Nemesis will be injecting based on the value in a load cell to the right of the actual load point on the engine.

The final and most likely cause for the engine to run very rich is that the fuel map is telling it to inject too much fuel. You will need to go to the main fuel map and begin to pull fuel out around the area where the engine is idling until the rich condition is fixed. If you have the wideband option and you have it connected, adjust the cells at and around the area where the yellow highlighted square indicating which cells the Nemesis is consulting while the engine idles until the 'AFR' reading hovers near 14.7. If you only have the stock oxygen sensor, watch the left 'O2' bar carefully. When you reach the point at which the bar goes from '1' to '0,' you have found the ideal location to idle the engine. You will most likely need to have someone drive the car around while you make the same adjustments to the cells in the driving range. Stay out of boost and make no adjustments at or near the boost range of the map unless you know what you are doing. Most engines will operate very well with identical values in each RPM row between full vacuum and up to around 50mm Hg from the 2500 RPM range up to redline. Because of this, you can have the driver hold a steady 3000 RPMs while you adjust each load point to 14.7 as you did with the idle range. Adjust the RPM row above and below the one that your have the engine at to the same value as the target row because you are very rarely right on the very top of the row you are adjusting, but usually off to one side or the other. Hills and/or a careful application of the brakes can be used to increase the load on the engine while maintaining a constant RPM. Do not worry too much about the lower load point which you cannot reach unless the engine is in full deceleration for now. Once you have a good set of cell settings, copy those values all across the driving range of the map from 2500 to redline. The car should now drive very well around town off boost. You should then have the driver do some easy driving in the sub 2500 RPM range to make some adjustments there as well to prevent the car from smoking or bucking while you transition between idle and steady driving.

Engine starts but won't settle into a steady speed

This section is for to deal with problems with your idle speed going up and down fairly dramatically and sharply. If you have large cams, you can expect your idle to bounce up and down almost constantly by about 50 or even as much as 100 RPMs, particularly if you try to idle the engine below 1000 RPM. That problem is not a fueling problem and this section does not address it.

You will first have to disable closed loop by going to 'Select->Settings' and clicking 'CLOSE LOOP' and unchecking the 'ENABLE CLOSED LOOP' box. If this solves the problem, you either have a map that is too far off 14.7:1 AFR and the close loop adjustments are preventing the engine from settling down to a good idle point or your injectors are too big and open too slowly to let you idle at 14.7:1 AFR. Look at the AFR if you have a wideband and using the fuel map and the down arrow key pull out fuel until the engine is idling around 14.5:1 AFR without close loop. If you don't have a wideband, do the same while watching the narrowband O2 reading. The narrowband voltage will be 1.0 when it is richer than 14.7:1 and then drop quickly to 0.1 as you go leaner than 14.7:1. Lean out the fuel in the idle range slowly until the narrowband switches to lean and then richen it again slightly so that it stays slightly rich. It is very important that you adjust the group of boxes on the fuel map surrounding the point at which the engine is idling and not just the box highlighted by the program. You do not want to create a big peak or hole anywhere in your fuel map, but a rolling terrain that is smooth. If the engine starts to go into oscillation as you lean it out and you have large injectors, you may need to set the idle so that it stays rich enough to keep the idle steady. In which case, set the 'LOWER RPM LIMIT' in the closed loop panel to around 1200 RPMs if you are using the narrowband as your closed loop sensor or adjust the 'Select->AFR target' map if you are going to use the wideband sensor and put in AFR values in the idle region of the map that are rich enough to keep the injectors from trying to inject less fuel than they minimally can during idle. When you have achieved a stable idle, continue to adjust it by loading the engine with the headlights, brake pedal and A/C to make sure that the idle stays smooth even under these load conditions. When the proper stable idle has been obtained and the proper parameter changes made, turn the closed loop back on and insure that the engine continues to idle properly.

If the problem persists, go to 'Select->Settings' and click on 'ISC.' Note down the 'MIN PWM DUTY' and 'MAX PWM DUTY' values so that you can set them back later. Set the 'MIN PWM DUTY' value to 30 and click 'enter' and set the 'MAX PWM DUTY' to 31 and click 'enter.' This will give the idle speed control valve a very small range to operate in so that it cannot contribute to the oscillations of the engine. If the engine settles down immediately, then you probably have to adjust you idle speed parameters, which is covered in another section. If the engine does not settle down immediately, check very carefully for any vacuum leaks around your intake manifold, fuel injection ports and the vacuum hoses connected to the intake manifold.

The ignition timing map can also cause the engine to oscillate somewhat and not settle down. In general, you want the ignition timing to decrease steadily as the RPMs drop and increase steadily as the RPMs increase, but right around the idle region it is sometimes useful to add a degree or two of timing in RPM point right below where you want the engine to idle in order to help the engine jump back up to the desired idle point if it drops back temporarily. Avoid abrupt changes to the timing across neighboring cells. Also, a little less timing tends to calm the engine down while too much timing around idle makes it less steady. Proper idle timing on the 3S-GTE should be around 14-18 degrees with stock and mild cams and 18-24 degrees with large cams. If you change the timing at idle, go back and re-visit the fuel settings since timing changes have some effect of fuel requirements.

Once you seem to have a set of maps that operate the engine steadily, go back and set the 'MIN PWM DUTY' and 'MAX PWM DUTY' values back to normal (usually 2 and 98). If this causes the problem to start again, then the idle speed valve is likely to blame.

Engine takes one or two tries to start when cold

This condition is most usually caused by either too much or not enough post start enrichment. Bring your laptop out with you when the engine is cold and connect it to the Nemesis before you start the engine. Look at the 'COOL' reading to determine the temperature of the coolant. Go to 'Select->Control 1->Post start enrichment' to see how much enrichment the Nemesis is providing after the engine starts. Depending on the temperature of the coolant when the engine starts, the Nemesis increases the amount of fuel that it would normally inject by the amount specified. This enrichment decreases steadily over the span of about a minute to zero. Although every setup is going to be somewhat different, you should normally expect to have to add somewhere around 40-60% enrichment when the engine coolant starts at 20C. This enrichment should be at or very near zero at 70C. If the engine stalls but starts right up again when cranked it probably does not have enough fuel enrichment. If it stalls and seems to have a hard time starting again unless you push the throttle wide open to clear the flooded state then you are probably giving it too much fuel.

Idle speed issues

The Nemesis controls the stock idle speed valve directly but unlike the stock ECU it does not use the fourth wire on the stock TPS to know when the throttle is at the idle position. For this reason, the TPS calibration process must be performed. If your system is not controlling idle speed or if the idle speed valve is always open and leaking boost the most likely reason is that you have not calibrated the TPS.

Another possibility for the Nemesis not controlling idle speed properly is that the 'MAX VACUUM (mmHg)' value in the 'Select->Settings' panel under the 'ISC' section is not set to a value that is lower than the amount of vacuum that the engine is producing at warm idle. Allow the engine to warm up and set this value to a value at least 50 larger than the amount of vacuum the engine produces when idling.

If the idle speed when the engine is warm is near the target speed but the idle speed when the engine is cold is too low, the idle screw on top of the throttle body needs to be turned counterclockwise to allow more air to enter the intake manifold. Warm up the engine and while it is idling with the headlights and accessories off (if you have a Canadian model which always has the headlights on, leave them on), turn the screw counterclockwise until the engine starts to idle above the target range and then turn it clockwise until the idle speed is right on the target range.

Go to 'Select->Settings' and click the 'ISC' button. The 'PROPORTIONAL' value determines how strongly the Nemesis adjusts idle speed. Set this value to the highest number that does not produce any wavering or hunting of the idle speed. This hunting will be particularly noticeable when the engine is first warming up, because that is when the Nemesis has to control the largest amount of air. The 'INTEGRAL' value determines how much the Nemesis will flare the engine when the engine first starts and how quickly it attempts to recover idle speed when the engine is allowed to drop quickly back to idle. Set this value so that the initial flare of the engine when you start it is about 1800RPMs. The 'DERIVATIVE' value determines how far the Nemesis will allow the idle to be from the desired set point before calculating a new idle speed valve opening. Set this value so that the initial flare at startup comes down within a couple of seconds after the engine starts and the idle speeds stays within a reasonable range of the desired target without constant wavering.

The idle target is set by going to 'Select->Control 2->Idle speed target.' This map determine the idle speed target based on engine coolant temperature. Set this map so that the engine idles between 1600-1200RPM when it is cold and around 1000-800RPMs when it warms up. Keep in mind that the engine normally requires a lot more air just to idle at the same speed when it is cold as when it is warm, therefore there is a limit to how wide an RPM range you can expect to get between cold idle and warm idle. A 400 RPM difference is about the limit and even this requires a little bit of help from yet another map. Go to 'Select->Control 2->Coolant temp spark trim' and on the base maps we provide you will note that a few extra degrees of timing are added when the engine is cold. This extra timing helps the engine idle a little faster when it is cold and allows it to drive a little better when it is warming up.

If the engine still does not want to idle faster when it is cold, make sure that the post-start enrichments, coolant temp trims and ignition timing are appropriate for the engine. Too much enrichment will bog the engine down and keep it from idling well or driving well when it is cold. Insufficient enrichment will also affect cold idle and drivability. If these settings are good, then you may need to turn up the 'PROPORTIONAL' value to make the Nemesis more aggressive about controlling the idle speed.

Engine hesitates and stutters under boost

The most likely reason is that the Nemesis is detecting knock and pulling timing. If this is the case you need to determine if you are indeed getting knock or if your knock threshold is set much too conservatively. If you can hear a rattling sound then you may actually be getting knock and you need to quickly address that by adding more fuel or taking out timing until the condition stops. If you do not hear knock, then go to 'Select->Control 1->Knock threshold' and have somebody drive the car and boost a little bit while you watch the little white crosses that indicate how much of a knock signal the Nemesis is receiving. If any crosses are appearing above the knock threshold curve, the Nemesis will retard timing. You will also see the 'ADV' bar on the main screen turn red whenever the Nemesis retards timing due to knock. If are unsure if the level of knock you are getting is safe, put in a tank of high octane race fuel and see what kind of knock response values you are getting then. Remember that it is normal for the knock sensor to give a signal as it reacts to normal engine operation. The signal will be stronger in the presence of real knock. Once you determine what the normal signal level is without knock, set the threshold curve so that it is a little above the highest of the normal engine noise. Normally, the noise will be somewhat lower at lower RPMs, so you can make the threshold curve lower at lower RPMs. You can also see the knock response signal level and how much retard the Nemesis is applying in response to knock on the datalog.

Power cuts out under boost

The Hydra Nemesis 2.1 and 2.5 implements a boost cut feature at 3 psi above the boost target set in the boost target table. Go to 'Select->Control 2->Boost target' and set the boost target to a level that is suitable for your setup. The Hydra Nemesis 2.6 has a separate 2D table to indicate the boost cut point. Select 'Map Group->2D Boost control' and then 'Map->Maximum boost' and set the boost target to a level that is suitable for your setup.