How to decide which ensemble (NVE, NPT or NVT) is suitable for Molecular Dynamic simulations of Protein-Ligand complex and is it necessary to go through NVT ensemble before moving on to NPT ensemble for simulations of Protein-Ligand complex? If so then what is the main purpose of doing NVT before NPT?
The ensemble you choose needs to align with whatever real-world conditions you wish to simulation. As Behnam has pointed out, this is usually NPT for most biological/biophysical simulations.
It is common to equilibrate simulation systems in multiple steps, first NVT, then NPT, for algorithmic stability. If one initializes random velocities while simultaneously turning on a barostat, the initial fluctuations in the box volume may be very large and potentially unstable. Thus it is common to equilibrate the velocity distribution at a constant temperature under an NVT ensemble, before moving to NPT. This is by no means required, but it is a robust protocol that is widely used.
The isothermal–isobaric (NPT) ensemble is best, since it 'corresponds most closely to laboratory conditions'.*)
*) See the attached Wikipedia entry.
https://en.wikipedia.org/wiki/Molecular_dynamics
The ensemble you choose needs to align with whatever real-world conditions you wish to simulation. As Behnam has pointed out, this is usually NPT for most biological/biophysical simulations.
It is common to equilibrate simulation systems in multiple steps, first NVT, then NPT, for algorithmic stability. If one initializes random velocities while simultaneously turning on a barostat, the initial fluctuations in the box volume may be very large and potentially unstable. Thus it is common to equilibrate the velocity distribution at a constant temperature under an NVT ensemble, before moving to NPT. This is by no means required, but it is a robust protocol that is widely used.
It depends on which barostat and thermostat you are using when it comes to algorithmic stability.
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