I dunno LogicWorks, and i guess eagle is not what you are looking for... If you do not find what you are looking for on http://freshmeat.net/ there likely is no such program for free for linux
I think I have found something. It's called 'Electric' and is made by StaticFree Software. It's able to tie into Spice and Irsim. It also has a built in similator and can be connected to some other engines I'm not familar with.
I'm looking at Eagle right now though and it seems interesting.
Also, if you're using Matlab and would like a free alternative, check out https://www.gnu.org/software/octave/ This program is quite compatible with Matlab.