In all the simulations I am using:
i) 2dim system periodic 1 1 0
ii) blx bly blz = 2.5*diam
iii) Generalized LJ potential to mimic hard core interaction
First simulations I was using:
i) rigid bond command for the dimers (dumbbells) => No virtual sites
ii) Langevin Dynamics Thermostat
Current Simulations I will try:
i) Harmonic Bonds with high K value (but temperature seems to be dependent of such value!)
ii) DPD thermostat
I want to reproduce (qualitatively) some experimental results. So, I am really interested in performing the simulations with the correct parameters and methodologies.
In your email you mentioned: "bond length constraint thing... should be a RATTLE or SHAKE implementation. I'm not exactly sure how it works and I'm not sure if it works..."
This means that using rigid bonds or even harmonic bonds in a 2Dimensional system is not a good idea?
When I used rigid bond command, I was able to reproduce some structural properties and the system "looks fine". The lentgh bond is keeped constant, temperature is preserved and total energy is almost just kinetic energy. However I am interested in dynamical properties...
I would really appreciate any advice or suggestion.
Thanks a lot