10 Applications of Molecular Dynamics Simulations …
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In the 1980s, MD simulation algorithmic improvements allowed for simulation and
calculation of the free energy of macromolecules and protein complexes [39–41]. In
the 1990s, high-temperature MD simulations successfully characterized the dynamic
changes of macromolecules and captured the ensemble of structures based on the
time scale [42]. Thanks to improvement in algorithms and computational power, MD
simulations were additionally employed to study intermolecular interactions. Among
various theoretical techniques, MD simulation is one of the widely used techniques
across various research fields and is thus highly cited [43]. Presently, the number
and scale of simulation techniques have expanded greatly. Using modern tools, a
researcher can run a microsecond-scale simulation of solvated protein and protein
complexes such as protein-nucleic acid, protein–protein, protein–small molecules,
and protein or protein complexes immersed in a lipid layer. These simulations allow
the field to answer questions around binding modes and thermodynamics of a small
molecule, as well as folding and structural changes of a protein.
10.3 Types of MD Simulations
10.3.1 All-Atom Simulations
All-atom stimulations are run with simulation packages including NAMD, GROMACS, and AMBER. These packages determine molecular structure, conformational analysis, and the dynamic property of proteins, protein complexes, lipid layers,
and polymers. The main drawback or limitation of all-atom simulations is the time
and computational cost. All-atom MD simulations explicitly represent each atom
in solutes and solvents, which drives up the computational cost. To overcome this
limitation, coarse-grained simulation methods were developed.
10.3.2 Coarse-Grained Simulations
A coarse-grained simulation models large-scale protein or protein complex models and enables longer time-scale simulations by increasing the order of magnitude
compared with all-atom simulations. Therefore, coarse-grained simulation is an alternative and effective method when compared to all-atom stimulation. Coarse-grained
simulation can be run using a common MD simulation package by applying a specific coarse-grained force field. In this kind of simulation, a small group of residues
or atoms in the simulated system are treated as a single particle rather than individual atoms. By leveraging this speed-up of fewer degrees of freedom, coarse-grained
simulations are faster than all-atom simulations. The running time of an MD simulation depends on the frequencies of motion including bond stretching, side chain and
loop motion, and angle bending. Water molecules are not explicitly simulated here.
185
In the 1980s, MD simulation algorithmic improvements allowed for simulation and
calculation of the free energy of macromolecules and protein complexes [39–41]. In
the 1990s, high-temperature MD simulations successfully characterized the dynamic
changes of macromolecules and captured the ensemble of structures based on the
time scale [42]. Thanks to improvement in algorithms and computational power, MD
simulations were additionally employed to study intermolecular interactions. Among
various theoretical techniques, MD simulation is one of the widely used techniques
across various research fields and is thus highly cited [43]. Presently, the number
and scale of simulation techniques have expanded greatly. Using modern tools, a
researcher can run a microsecond-scale simulation of solvated protein and protein
complexes such as protein-nucleic acid, protein–protein, protein–small molecules,
and protein or protein complexes immersed in a lipid layer. These simulations allow
the field to answer questions around binding modes and thermodynamics of a small
molecule, as well as folding and structural changes of a protein.
10.3 Types of MD Simulations
10.3.1 All-Atom Simulations
All-atom stimulations are run with simulation packages including NAMD, GROMACS, and AMBER. These packages determine molecular structure, conformational analysis, and the dynamic property of proteins, protein complexes, lipid layers,
and polymers. The main drawback or limitation of all-atom simulations is the time
and computational cost. All-atom MD simulations explicitly represent each atom
in solutes and solvents, which drives up the computational cost. To overcome this
limitation, coarse-grained simulation methods were developed.
10.3.2 Coarse-Grained Simulations
A coarse-grained simulation models large-scale protein or protein complex models and enables longer time-scale simulations by increasing the order of magnitude
compared with all-atom simulations. Therefore, coarse-grained simulation is an alternative and effective method when compared to all-atom stimulation. Coarse-grained
simulation can be run using a common MD simulation package by applying a specific coarse-grained force field. In this kind of simulation, a small group of residues
or atoms in the simulated system are treated as a single particle rather than individual atoms. By leveraging this speed-up of fewer degrees of freedom, coarse-grained
simulations are faster than all-atom simulations. The running time of an MD simulation depends on the frequencies of motion including bond stretching, side chain and
loop motion, and angle bending. Water molecules are not explicitly simulated here.