Section 20.1.3.1. Energetic properties

In Fig. 20.1.3.1, the non-bonded contributions to the total potential energy are shown. The non-bonded interactions comprise Lennard–Jones and electrostatic interactions. Solvent–solvent, solute–solute and solute–solvent interaction energies are shown separately. All of these appear converged after approximately 100 ps. The solvent–solvent energy remains close to its initial value during the whole simulation, the water molecules having relaxed during the pre-equilibration period, while the protein was restrained. The protein internal energy increases during the first few hundred picoseconds, but this is compensated by a decrease in the protein–solvent energy as the protein adapts to the force field and the pre-relaxed solvent environment. This effect becomes negligible after about 200 ps, from which time point the system can be viewed as equilibrated with respect to the energies. The distribution of kinetic versus potential energy and the total (bonded and non-bonded) energy of the system relaxes even faster (results not shown).

Figure 20.1.3.1| top | pdf | Non-bonded energies (in kJ mol−1) of the simulated system as a function of time.