Dear Donya Ramimoghadam,

I think the following links may be helpful.

http://espressomd.org/html/ess2012/Day2/T1-01-IntroToES/talk.pdf

http://as.wiley.com/WileyCDA/WileyTitle/productCd-3527324151.html

http://web.pa.msu.edu/people/duxbury/courses/phy480/BaschnagelReview2004.pdf

Thanks.

Generally every established MD engine is sufficiant for simulating polymers, especially when realizing that proteins or DNA are polymers, too.

Away from that, what is more important in case of polymers without extisting forcefields or parameters is the respective toolchain to parameterize new molecules. Here, e.g. CgenFF + VMD + NAMD or Gaussian + AmberTools(GAFF2) + NAMD/SANDER migth be reasonable choices.

All the MD simulation codes serve almost the same purposes.

You can start with Lammps (http://lammps.sandia.gov/), which is an interesting code by Steve Plimpton.