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S. Sakkiah et al.
details about solute molecule fluctuation in the solvent density. Explicit models such
as SPC and TIP3P are used in most MD simulation programs and detail the solvent
spatial descriptions. Membrane proteins should be inserted into a pre-equilibrated
lipid layer. After system assembly in solute or lipid, new topology files are built to
run energy minimization and reduce van der Waals interactions.
10.5.5 Adding Ions
A molecular system should be solvated in a pre-equilibrated water box. The protein
in the solvated water box might carry a charge. Hence, the system is neutralized by
adding ions including Na
+ , Cl
− , and K
+ . Positive ions are employed for systems with
negative charge and vice versa.
10.5.6 Minimizing Structure
Energy minimization is a crucial step in MD simulations. This step configures the
protein system to be stable and removes bad clashes between the solute and solvent,
as well as filtering out inappropriate geometry.
10.5.7 Establishing Equilibration Dynamics
A reasonable structure obtained from energy minimization is required to continue the
simulation. Equilibration is an important step preceding the production run. The main
purpose of equilibration is to reduce non-equilibrium effects and to avoid or reduce
structural distortions. The protein (embedded in the box of explicit system solvents)
is fixed, and water molecules are permitted to move about the protein. Once the water
molecules are equilibrated, the protein constraint is removed and the whole system
is equilibrated together. MD simulation begins in earnest only when the system
equilibrates the ions and solvents around the protein. There are three ensembles in
the equilibration run: (i) NVE, constant number of the particles, volume, and total
energy; (ii) NVT, constant number of particles, volume, and temperature; and (iii)
NPT, constant number of particles, volume, and temperature. In the NVT ensemble,
the thermostat maintains the system temperature to reach a desired value. Next, NPT
stabilizes system pressure. The final production run is executed only when the system
is temperature and pressure stable.
S. Sakkiah et al.
details about solute molecule fluctuation in the solvent density. Explicit models such
as SPC and TIP3P are used in most MD simulation programs and detail the solvent
spatial descriptions. Membrane proteins should be inserted into a pre-equilibrated
lipid layer. After system assembly in solute or lipid, new topology files are built to
run energy minimization and reduce van der Waals interactions.
10.5.5 Adding Ions
A molecular system should be solvated in a pre-equilibrated water box. The protein
in the solvated water box might carry a charge. Hence, the system is neutralized by
adding ions including Na
+ , Cl
− , and K
+ . Positive ions are employed for systems with
negative charge and vice versa.
10.5.6 Minimizing Structure
Energy minimization is a crucial step in MD simulations. This step configures the
protein system to be stable and removes bad clashes between the solute and solvent,
as well as filtering out inappropriate geometry.
10.5.7 Establishing Equilibration Dynamics
A reasonable structure obtained from energy minimization is required to continue the
simulation. Equilibration is an important step preceding the production run. The main
purpose of equilibration is to reduce non-equilibrium effects and to avoid or reduce
structural distortions. The protein (embedded in the box of explicit system solvents)
is fixed, and water molecules are permitted to move about the protein. Once the water
molecules are equilibrated, the protein constraint is removed and the whole system
is equilibrated together. MD simulation begins in earnest only when the system
equilibrates the ions and solvents around the protein. There are three ensembles in
the equilibration run: (i) NVE, constant number of the particles, volume, and total
energy; (ii) NVT, constant number of particles, volume, and temperature; and (iii)
NPT, constant number of particles, volume, and temperature. In the NVT ensemble,
the thermostat maintains the system temperature to reach a desired value. Next, NPT
stabilizes system pressure. The final production run is executed only when the system
is temperature and pressure stable.