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What is the best electronic circuit simulation EDA program for Linux?

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Do you asking for open source replacements, or simply all possible software?

Cadence virtuoso suite is dedicated to work only on unix platforms and is possible to simulate not only ICs but also discrete electronics, with many different simulators like spectre, HSpice, eldo, etc.

From open source tools usually ngspice is recommended as simulator, while many graphical front-ends are used for schematic.
 

I use ngspice because it contains analog, digital and mixed signal simulation. You can use kicad to generate netlists too.
 
I design schematic/PCB in KiCAD and use gEDA(Ngspice) for Mixed-Mode Simulation.
You can also use LT-Spice but you will have to to use Wine. Linear Technologies haven't release Linux binary version of LT-Spice.
KiCAD - Ngspice pair is quite dependable. We use them for professional industrial project.
 
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