186
S. Sakkiah et al.
Due to the above mentioned reasons, coarse-grained simulation is best employed
for long time-scale simulations. The drawbacks of this approach include: (i) loss
of atomic resolution, (ii) less accurate energetic estimation compared with atomistic approaches, (iii) limited availability of force fields, and (iv) need for additional
stimulations to obtain atomistic trajectory details.
10.3.3 Classical MD
Nowadays, classical MD simulations are used to investigate many properties of
molecular systems. Classical MD simulations calculate the movement of particles
from an initial input structure throughout the simulation. Interactions of each particle
in the simulation system with all other particles are calculated by the total force acting on a given particle. The new position of each atom after a specific time interval
is determined by acceleration, previous position, and velocity. Classical MD simulations are best applied to understand protein structure and function or to propose
hypotheses based on experimental data. The electronic distribution from classical MD
is relatively like the coarse-grained MD method. If the interaction site has assigned
fixed partial charges and an approximate model for polarization effects, the motion
of electrons is not dominated by a time scale. The main limitation of classical MD
simulation is the system size and time scale.
10.4 MD Simulation Software
A panoply of MD simulation packages has been developed over the years. The
most popular packages include GROningen MAchine for Chemical Simulations
(GROMACS) [44], Assisted Model Building with Energy Refinement (AMBER)
[45], NAnoscale Molecular Dynamics (NAMD) [46], TINKER [47], CHARMM
[48], LAMMPS [49], DL_POLY [50], MOLDY [51], and Desmond [52]. Some
MD simulation packages have their own force fields, while others only provide MD
simulation algorithms and require suitable force fields as input. The GROMACS,
CHARMM, NAMD, GROMACS, and AMBER packages predominate biomolecular simulations. AMBER and CHARMM have their own force fields and provide
various scripts to run and analyze simulations [53, 54]. GROMACS and NAMD
show remarkable efficiency for large-scale biomolecular simulations. GROMACS
[55], AMBER [54], and CHARMM [53] have coarse-grained force fields. NAMD
supports only standard force fields such as AMBER and CHARMM. Desmond is a
newcomer software package from D.E. Shaw Research which supports force fields
including AMBER, CHARMM, and POLS-AA [56]. As examples, Figs. 10.1, 10.2,
10.3 and 10.4 give an MD simulations protocol overview for GROMACS, AMBER,
Desmond, and NAMD.
S. Sakkiah et al.
Due to the above mentioned reasons, coarse-grained simulation is best employed
for long time-scale simulations. The drawbacks of this approach include: (i) loss
of atomic resolution, (ii) less accurate energetic estimation compared with atomistic approaches, (iii) limited availability of force fields, and (iv) need for additional
stimulations to obtain atomistic trajectory details.
10.3.3 Classical MD
Nowadays, classical MD simulations are used to investigate many properties of
molecular systems. Classical MD simulations calculate the movement of particles
from an initial input structure throughout the simulation. Interactions of each particle
in the simulation system with all other particles are calculated by the total force acting on a given particle. The new position of each atom after a specific time interval
is determined by acceleration, previous position, and velocity. Classical MD simulations are best applied to understand protein structure and function or to propose
hypotheses based on experimental data. The electronic distribution from classical MD
is relatively like the coarse-grained MD method. If the interaction site has assigned
fixed partial charges and an approximate model for polarization effects, the motion
of electrons is not dominated by a time scale. The main limitation of classical MD
simulation is the system size and time scale.
10.4 MD Simulation Software
A panoply of MD simulation packages has been developed over the years. The
most popular packages include GROningen MAchine for Chemical Simulations
(GROMACS) [44], Assisted Model Building with Energy Refinement (AMBER)
[45], NAnoscale Molecular Dynamics (NAMD) [46], TINKER [47], CHARMM
[48], LAMMPS [49], DL_POLY [50], MOLDY [51], and Desmond [52]. Some
MD simulation packages have their own force fields, while others only provide MD
simulation algorithms and require suitable force fields as input. The GROMACS,
CHARMM, NAMD, GROMACS, and AMBER packages predominate biomolecular simulations. AMBER and CHARMM have their own force fields and provide
various scripts to run and analyze simulations [53, 54]. GROMACS and NAMD
show remarkable efficiency for large-scale biomolecular simulations. GROMACS
[55], AMBER [54], and CHARMM [53] have coarse-grained force fields. NAMD
supports only standard force fields such as AMBER and CHARMM. Desmond is a
newcomer software package from D.E. Shaw Research which supports force fields
including AMBER, CHARMM, and POLS-AA [56]. As examples, Figs. 10.1, 10.2,
10.3 and 10.4 give an MD simulations protocol overview for GROMACS, AMBER,
Desmond, and NAMD.