Article ID: 187 - Last Modified: December 4, 2010
What ensemble should I use for my molecular dynamics simulation in Desmond?
Most simulations are carried out in the Isothermal-Isobaric ensemble (NPT). However, to equilibrate a system correctly, it is necessary to run a short simulation in the NVT ensemble until a suitable temperature is reached, as the calculation of pressure is inaccurate at low temperatures. Selecting "Relax Model System Before Simulation" in the Desmond Molecular Dynamics GUI will automatically perform this pre-NPT equilibration.
Keywords: Molecular dynamics, ensemble, pressure, NPT, NVT
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