Question

In langevin dynamics, equations of motions are modified to incorporate the viscosity of the solution and the effect of collisions between molecules. Allows effect of water to be modelled without modelling each atom. What are the computational advantages of using langevin dynamics over Molecular dynamics?

Natural Statistical ensemble for MD simulation is NVT, but often NVE and NPT are implemented. What additional factors need to be included for these to be implemented?

Answer 1

Molecular dynamics is a computer simulation method for analysing the physical movements of of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time for the dynamic evolution of system. In other words moving of atoms and molecules are determined by solving Newton's equation of motion. Forces between the particles and their potential energies are calculated using interatomic potentiality. It is used to describe the the patterns strength properties of protein behaviour. Molecular system consist many number of particles. It is impossible to determine the properties of such complex system. MD simulation solves this problem. However MD simulation contains lots of errors in numerical integration

Langevin dynamics is the mathematical modelling of dynamics of molecular systems. Molecular system contains friction causes air molecules, high velocity collision etc. Langevin dynamics tries to extend MD to allow for these effects.It effect the temperature to be controlled. It imitates the viscous aspect of solvent for denser solvent hydrodynamic interaction were not detected through Langevin dynamics

In MD simulation does not integrate the partition function for to compute the probability directly. This is due to large number of degrees of freedom. The advantage of MD is that only the energy needs to be calculated not the forces.

Langevin dynamics is more accurate compared to molecular dynamics. It also affects the fast kinetics and this method is formally completely correct.

There are 4 ensemble which are commonly used in molecular simulation. These are indicated by the three thermodynamics quantities which are kept constant. The ensembles are constant-NVE or microcanonical ensemble, constant NVT or canonical ensemble, constant-NPT or isothermal-isobaric ensemble, $\mu$ VT or grand canonical ensemble.Another possible ensemble is $\mu$ PT ensemble.

Methods for keeping the pressure constant in MD simulations are analogous to the temperature coupling method. The disadvantage of molecular dynamics simulations are it is unknown if an ensemble is generated.