Molecular Dynamics

BioCodeKb - Bioinformatics Knowledgebase

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. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanics force fields. The method is applied mostly in chemical physics, materials science, and biophysics.


The design of a molecular dynamics simulation should account for the available computational power. Simulation size (n = number of particles), timestep, and total time duration must be selected so that the calculation can finish within a reasonable time period. However, the simulations should be long enough to be relevant to the time scales of the natural processes being studied. To make statistically valid conclusions from the simulations, the time span simulated should match the kinetics of the natural process. Otherwise, it is analogous to making conclusions about how a human walks when only looking at less than one footstep. Most scientific publications about the dynamics of proteins and DNA use data from simulations spanning nanoseconds (10−9 s) to microseconds (10−6 s). To obtain these simulations, several CPU-days to CPU-years are needed. Parallel algorithms allow the load to be distributed among CPUs; an example is the spatial or force decomposition algorithm.


Another factor that impacts total CPU time needed by a simulation is the size of the integration timestep. This is the time length between evaluations of the potential. The timestep must be chosen small enough to avoid discretization errors (i.e., smaller than the period related to fastest vibrational frequency in the system). Typical timesteps for classical MD are in the order of 1 femtosecond (10−15 s). This value may be extended by using algorithms such as the SHAKE constraint algorithm, which fix the vibrations of the fastest atoms (e.g., hydrogens) into place.


For simulating molecules in a solvent, a choice should be made between explicit and implicit solvent. Explicit solvent particles (such as the TIP3P, SPC/E and SPC-f water models) must be calculated expensively by the force field, while implicit solvents use a mean-field approach. Using an explicit solvent is computationally expensive, requiring inclusion of roughly ten times more particles in the simulation. But the granularity and viscosity of explicit solvent is essential to reproduce certain properties of the solute molecules. This is especially important to reproduce chemical kinetics.


In all kinds of molecular dynamics simulations, the simulation box size must be large enough to avoid boundary condition artifacts. Boundary conditions are often treated by choosing fixed values at the edges (which may cause artifacts), or by employing periodic boundary conditions in which one side of the simulation loops back to the opposite side, mimicking a bulk phase.


Molecular dynamics can be used to explore conformational space, and is often the method of choice for large molecules such as proteins. In molecular dynamics the energy surface is explored by solving Newton's laws of motion for the system. A common strategy when searching conformational space is to perform the simulation at a very high, physically unrealistic temperature as this enhances the ability of the system to overcome energy barriers. Structures are then selected at regular intervals from the trajectory for subsequent energy minimization.


Molecular dynamics itself can be further divided into two classes: classical molecular dynamics and ab initio molecular dynamics. Classical molecular dynamics treats molecules as point masses and the interactions between molecules are represented by simple potential functions, which are based on empirical data or from independent quantum mechanical calculations. The so-called ab initio molecular dynamics unifies classical molecular dynamics and density-function theory, and takes into account the electronic structure when calculating the forces on atomic nuclei.


Tools

  • CHARMM

  • GROMACS

  • NAMD

  • Desmond

  • Amber


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