[Liverpool] 3d Programming

[Sujita Purushothaman]

Hi All,
   Can anyone recommend a programming language/package for 3d 
programming on Linux? I need to write a program that simulates movements 
of biological molecules, and I'm doing the programming on linux. I am 
totally new to 3D programming (as in I know nothing about it!). I don't 
need any textures, I only need to model ball and stick movements. I'm 
used to C and PHP, so learning a new language shouldn't be a problem.
   Thanks!

Rgds,
Sujita