Heating time, molecular dynamics

Analytical models of pore collapse follow two approaches, termed hydrodynamic [162] or viscoplastic. In Mader s hydrodynamic model [162] (Fig. 17a), a steep planar shock front hits the upstream surface of an empty spherical pore of diameter d (for nanopores, gas inside the pore can be neglected [52,162]), it accelerating the free surface to velocity 2Up [5]. The pore s free surface undergoes hydrodynamic focusing [61,162]. A material spike strikes the downstream surface, causing impact heating. In molecular dynamics simulations, individual molecules from the upstream surface are observed to break off and strike the downstream surface [61,163]. The hydrodynamic time constant for pore collapse is approximately the material transit time across the pore. 

In a molecular dynamics calculation, you can add a term to adjust the velocities, keeping the molecular system near a desired temperature. During a constant temperature simulation, velocities are scaled at each time step. This couples the system to a simulated heat bath at Tq, with a temperature relaxation time of "r. The velocities arc scaled bv a factor X. where... 

In many molecular dynamics simulations, equilibration is a separate step that precedes data collection. Equilibration is generally necessary to avoid introducing artifacts during the heating step and to ensure that the trajectory is actually simulating equilibrium properties. The period required for equilibration depends on the property of interest and the molecular system. It may take about 100 ps for the system to approach equilibrium, but some properties are fairly stable after 10-20 ps. Suggested times range from 5 ps to nearly 100 ps for medium-sized proteins. 

The choice of heating time depends on the purpose of the molecular dynamics simulation. If the simulation is for conformational searches, the heating step is not critical for a successful calculation. The heating step may be rapid to induce large structural changes that provide access to more of the conformational space. 

If the heating time t or cooling time t are non-zero, or if the run time tj. is non-zero and constant temperature is selected, velocities are adjusted (rescaled) during the molecular dynamics run to change the temperature of the system. 

The simplest method that keeps the temperature of a system constant during an MD simulation is to rescale the velocities at each time step by a factor of (To/T) -, where T is the current instantaneous temperature [defined in Eq. (24)] and Tq is the desired temperamre. This method is commonly used in the equilibration phase of many MD simulations and has also been suggested as a means of performing constant temperature molecular dynamics [22]. A further refinement of the velocity-rescaling approach was proposed by Berendsen et al. [24], who used velocity rescaling to couple the system to a heat bath at a temperature Tq. Since heat coupling has a characteristic relaxation time, each velocity V is scaled by a factor X, defined as... 

Concluding this section, one should mention also the method of molecular dynamics (MD) in which one employs again a bead-spring model [33,70,71] of a polymer chain where each monomer is coupled to a heat bath. Monomers which are connected along the backbone of a chain interact via Eq. (8) whereas non-bonded monomers are assumed usually to exert Lennard-Jones forces on each other. Then the time evolution of the system is obtained by integrating numerically the equation of motion for each monomer i... 

Markov decay time, Monte Carlo heat flow simulation, nonequilibrium molecular dynamics, 80-81... 

Nonequilibrium molecular dynamics (NEMD) Monte Carlo heat flow simulation, 71-74 theoretical background, 6 Nonequilibrium probability, time-dependent mechanical work, 51-53 Nonequilibrium quantum statistical mechanics, 57-58... 

These two methods are different and are usually employed to calculate different properties. Molecular dynamics has a time-dependent component, and is better at calculating transport properties, such as viscosity, heat conductivity, and difftisivity. Monte Carlo methods do not contain information on kinetic energy. It is used more in the lattice model of polymers, protein stmcture conformation, and in the Gibbs ensemble for phase equilibrium. 

Select the Molecular dynamics menu to open the dialog box. Specify Time, Temperature, and Step size for Heating cycle, Equilibrium period, and Cooling cycle. 

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