Contents
What is the time space scale associated with molecular dynamics simulation?
Simulations of solvated proteins are calculated up to the nanosecond time scale, however, simulations into the millisecond regime have been reported. Newton’s equation of motion can then relate the derivative of the potential energy to the changes in position as a function of time.
What is molecular dynamics simulation used for?
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic “evolution” of the system.
How to do a simulation of molecular dynamics?
Perform simulation until equilibration is reached (property dependent) Perform production simulation to collect thermodynamic averages, positions, velocities Analyze the results via post-processing Initialize: Initial particle positions, velocities
How are the properties of a MD simulation calculated?
A MD simulation generates a sequence of points in phase space connected in time The result is atrajectoryof all particles in the system as a function of time Time averages and other properties can be calculated from this trajectory Motion of the system through phase space is governed by Hamiltonian equations of motion : r˙ i= ∂H ∂p
How is phase space and time average in molecular dynamics?
Phase Space and Time Averages A system containingNatoms has 6Nvalues defining the state of the system (3Ncoordinates (r), 3Nmomenta (p)) Each combination of coordinates and momenta define a point in the 6N-dimensionalphase space : Γ N
Which is the most intensive task in molecular dynamics?
During a classical MD simulation, the most CPU intensive task is the evaluation of the potential as a function of the particles’ internal coordinates. Within that energy evaluation, the most expensive one is the non-bonded or non-covalent part. In Big O notation, common molecular dynamics simulations scale by