Equilibration

Equilibrating the system is often the next step after energy minimization.  For most systems, this process will involve allowing some solvent to relax around the solute of interest.  In many cases, the solvent is water, but it can also be a lipid bilayer, chloroform, etc.  Position restraints are often applied to the solute to keep its configuration more or less fixed while the system relaxes.

Equilibration is performed under the ensemble desired (NVT, NPT, etc) until all properties of interest have stabilized.  For instance, in NVT, once the temperature is stabilized, the system is equilibrated under this ensemble.  For NPT, the pressure and temperature should be stable before proceeding.

It is often advisable to perform equilibration using weak-coupling techniques for temperature and pressure, especially if your system is (potentially) far from equilibrium.  Using, i.e., the Nosé-Hoover thermostat for initial NVT equilibration can lead to wild oscillations of the temperature, with the system ultimately blowing up.