Slides

Sander: Pre-Equilibration
• 1. Classical restrained minimiza4on of the system
– acetone is restrained to its ini4al posi4on
– water molecules are allowed to reorient, i.e. to solvate the
solute properly (e.g. forming hydrogen bonds, ...)
• 2. Classical minimiza4on without restraints
• 3. Classical MD simula4on: Hea4ng / equilibra4on
– constant volume
– linear hea4ng (0 -­‐ 300 K)
– acetone is weakly restrained (water molecules can surround
the solute without forming holes)
– relaxa4on 4me: 300 ps (0.3 ns), (water relaxa4on 4me ≈10 ps)
• 4. Classical MD simula4on at 300 K and 1 atm (NPT)
– constant temperature (thermostat) and pressure (barostat)
– to adjust the density to its experimental value (≈1 g/cm 3 )