Yes, it is possible to simulate a trimer. I've previously performed MD simulation of hemoglobin (a tetramer).

Dear Chanin, thanks for reply,

Can you give a tutorial, or some link to follow?

Yup , it is possible to simulate trimer. Just use Pdb2gmx command . Gromacs will create  a topology file containing the topology of all chains.

hi you can simulate all that you want by using GROMACS!!!

Justin Lemkul has an excellent tutorial on using GROMACS. The group of Prof. Bonvin also has got some great step-by-step tutorial.

Links are appended below.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/

http://nmr.chem.uu.nl/~tsjerk/course/molmod/index.html#introduction

Thank you everyone!