28 September 2018 0 10K Report

I am running a simulation of a system with 72 peptides with low hydration (not completely solvated) using AMBER MD package. The system was minimised, NVT was performed followed by NPT at 1 atm, 300 K. The density of the system is close to 1.008 g/cm3. However, the experimental density of these polymers at the same hydration is 1.04-1.06 g/cm3. The simulation was performed with a box size of 200 A in each direction which compresses to 147 A during NPT. Why the density of polymer is always low in simulation? How to get the right density before again switching to NVT? Or should I run the simulation at high pressure to retain the density?

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