Hello, Jan!

As one of ways to simulate kinematics and dynamics of planar and spatial mechanical systems, Universal Mechanism could be used for your purposes.

http://www.universalmechanism.com/en/plugins/catalogue/index.php?id=14

http://www.universalmechanism.com/en/plugins/catalogue/index.php?id=9

It also has some interface of interaction with Matlab.

Regards!

If you want to simulate the dynamic and kinematic equation of a manipulator, I would suggest you to work with "User-Defined" block in Simulink-Matlab. Write the equations like a code, output the accelerations and double integrate to get the positions. This gives you complete freedom to write the equation as you want without any dependency on the toolboxes.

If you want to mechanically simulate without equations of motion, you can do so through any Mechanical or Multiphysics software like "SolidWorks, Ansys, COMSOL", etc.

you can this in MATLAB:

http://sirslab.dii.unisi.it/syngrasp/

or

http://graspit-simulator.github.io/