10 Applications of Molecular Dynamics Simulations …
189
Fig. 10.3 Steps involved in
molecular dynamics
simulations in NAMD
3. Determination of a solvate box: The commands Editconf and genbox define a
unit cell around a protein or protein complex and to fill said unit cell with water
molecules, respectively. Before energy minimization, the water molecules are
pre-equilibrated to remove water molecule overlap.
4. Energy minimization: A short minimization run removes large forces from structural distortions due to the addition of hydrogens and the broken hydrogen bond
network in water. The grompp command minimizes a solvated protein for two
reasons: (1) to remove local strains in the protein or protein complex due to
the addition of hydrogen atoms and (2) to remove bad van der Waals interactions. This command collects all parameters to run the minimization, topology,
and coordinate. It writes all results into a single tpr (portable binary run input)
file containing the starting structure, molecular topology, and parameters form
simulations.
5. Addition of ions: The pdb2gmx command also shows the charge of the protein.
The tpr file is an input for the genion command to add positive or negative ions
to neutralize the charged protein in the solvated system. The neutralized system
is subject to energy minimization using grompp command to remove severe
clashes.
6. Equilibration: The solvated system is equilibrated to avoid unnecessary protein
distortions in the simulation. In this step, heavy atoms of the protein are fixed at
189
Fig. 10.3 Steps involved in
molecular dynamics
simulations in NAMD
3. Determination of a solvate box: The commands Editconf and genbox define a
unit cell around a protein or protein complex and to fill said unit cell with water
molecules, respectively. Before energy minimization, the water molecules are
pre-equilibrated to remove water molecule overlap.
4. Energy minimization: A short minimization run removes large forces from structural distortions due to the addition of hydrogens and the broken hydrogen bond
network in water. The grompp command minimizes a solvated protein for two
reasons: (1) to remove local strains in the protein or protein complex due to
the addition of hydrogen atoms and (2) to remove bad van der Waals interactions. This command collects all parameters to run the minimization, topology,
and coordinate. It writes all results into a single tpr (portable binary run input)
file containing the starting structure, molecular topology, and parameters form
simulations.
5. Addition of ions: The pdb2gmx command also shows the charge of the protein.
The tpr file is an input for the genion command to add positive or negative ions
to neutralize the charged protein in the solvated system. The neutralized system
is subject to energy minimization using grompp command to remove severe
clashes.
6. Equilibration: The solvated system is equilibrated to avoid unnecessary protein
distortions in the simulation. In this step, heavy atoms of the protein are fixed at