I was wondering how I should interpret the results of my molecular dynamics simulation

Question

I ran a molecular dynamics simulation using forcite dynamics for polymers on graphene and a drug. The dynamics summary shows the total energy, potential energy,kinetic energy, total enthalpy, temperature, pressure, volume and density. The dynamics summary also shows the initial and final values along with the average and standard deviation.

For forcite dynamics and energy parameters I used ensemble (NVT), temp (298K), thermostat (Berendson), forcefield (compass), electrostatic and vanderwaals (group based), time (1000ps). I left everything else as default.

My prof mentioned that the drug should be loaded and released.

I used the same polymer and drug for each simulation but changed the concentration of the drug. I also used different ratios of the block copolymer. The polymers were placed on the graphene in the box.

I packed the box with water and placed the drug in the box manually.The drug wasn't released at the end of the simulation.

I'm confused about what the energies of the dynamics summary is supposed to tell me.

Answer 1

I couldn't completely understand your question, but I will mention some general back-of-the-napkin criteria to be sure that the MD simulation is doing what you think it is doing. These criteria are necessary but not sufficient.

• Visualize the initial, intermediate, and final structures to make sure you grabbed the correct structure and that the simulation isn't doing anything weird or unwanted.

• Make sure that after sufficient simulation time the energy profile reaches a plateau, i.e., the energy oscillates very little around some average value. The specification of "sufficient" and "very little" is highly dependent on the context. Usually, if the energy oscillations are too large, you may need to decrease the time step.

• Also make sure that the temperature and pressure reach a steady state. Temperature oscillations tend to be very little after sufficient simulation time (e.g., in the range of $\pm 10$ K for a target temperature of 300 K), whereas pressure oscillations tend to be rather large (e.g., in the range of $\pm 2$ kbar for a target pressure of 0 bar). Usually, if the temperature or pressure oscillations are larger than those ranges, you may need to increase the simulation box size.

• Try different time steps, different simulation box sizes and different thermostat/barostat damping parameters to see if these affect your results.

• Check the units!