16 Questions
What does the initialization process for ab initio molecular dynamics involve?
Setting initial positions and velocities compatible with the structure to be studied.
Why are initial velocities in molecular dynamics often set to zero or small?
To enable thermalization through increasing the temperature according to Maxwell-Boltzmann distribution.
What is the purpose of avoiding overlap and short distances in setting initial positions for molecular dynamics simulations?
To ensure proper interactions between atoms.
What type of differential equations are involved in the initialization process for molecular dynamics simulations?
Second order differential equations
What are reduced units used for in computational nanomechanics?
To improve computational efficiency by scaling all quantities to a few fundamental units.
In the context of computational nanomechanics, what does 'ab initio' refer to?
'From the beginning' or 'from first principles' simulations.
Which type of boundary condition is commonly used in molecular dynamics simulations to mimic an infinitely repeating system?
Periodic BCs
What type of interactions are represented by 3-body covalent interactions in molecular force fields?
Angle-bending interactions
What is the purpose of the Verlet list in molecular dynamics simulations?
To identify bonded atom pairs within a specific cutoff radius
In molecular force fields, what do hybrid orbitals and torsional potentials primarily influence?
Covalent bond lengths
What is the main role of linked lists in molecular dynamics simulations?
To efficiently manage non-bonded interactions
Which interaction type is primarily influenced by the functional forms for van der Waals forces in molecular simulations?
Dispersion forces
What do covalent interactions in molecular force fields primarily govern?
Chemical bond formation and breaking
What is the key role of atom type parameters in molecular force fields?
To describe the interaction strengths between different atom types
Which type of computational method is often used to compute interatomic potentials in molecular dynamics simulations?
Ab initio methods
What are conserved quantities associated with in classical mechanics?
Time-independent systems
Test your knowledge on computational nanomechanics, classical mechanics, and molecular dynamics simulations taught by Mir Masoud Seyyed Fakhrabadi at the University of Tehran.
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