MOLECULAR MODELLING AND DRUG DESIGN Question Papers (Regular, November 2007, RR)

SET :1

1. What are partial atomic charges? How they are related to the electrostatic potential of a molecule? [6+10]
2. Explain the following :
(a) simple water models
(b) flexible water models. [8+8]
3. Metropolis method is a non-deterministic method. Explain? [16]
4. What are order parameters? Describe their use in molecular simulations. [6+10]
5. (a) Describe Newton’s Laws of motion
(b) Describe the three types of situations in molecular dynamics to which Newton’s laws of motion may be applied.
(c) Explain the hard-sphere model of molecular dynamics
(d) Explain the square well potential method of molecular dynamics. [4+4+4+4]
6. Explain the difference between constraints and restraints and how they are used in a molecular dynamics simulation. [8+8]
7. Derive an expression for canonical partition function of a real gas. [16]
8. Explain the following :
(a) cut off region
(b) preferential sampling procedure
(c) force-bias Monte Carlo method
(d) Smart Monte Carlo method. [4+4+4+4]


SET :2

1. Explain the importance of out-of-plane bending in describing the geometry of molecules. [16]
2. What are Van der Waals potential functions? How they are used in modeling Van der Waals interactions. [6+10]
3. Explain in brief the concept of boundaries in molecular systems. [16]
4. What is Ewald Summation method? How is it useful in a molecular simulation program. [4+12]
5. Explain the following :
(a) Gear algorithm
(b) Rehman algorithm. [8+8]
6. What are the difficulties associated with the simulation of conformationally flexible molecules? Describe how they are dealt with. [6+10]
7. What is Monte Carlo Simulation? Why is it called so? How is it different from molecular dynamics simulation? What kind of technique it uses? [4+4+4+4]
8. Describe the Monte Carlo method of simulation of solute-solvent system. [16]


SET :3

1. What is polarization? What is its importance in molecular modeling? [6+10]
2. Explain the following :
(a) simple water models
(b) flexible water models. [8+8]
3. Explain the following :
(a) heat capacity and molecular simulation
(b) virial of a real system
(c) pair distribution function
(d) radial distribution function. [4+4+4+4]
4. What is a block method in a molecular simulation program? Describe its use and importance in improving the molecular simulation programme. [4+12]
5. (a) Describe Newton’s Laws of motion
(b) Describe the three types of situations in molecular dynamics to which Newton’s laws of motion may be applied.
(c) Explain the hard-sphere model of molecular dynamics
(d) Explain the square well potential method of molecular dynamics. [4+4+4+4]
6. What is relaxation time? How is it used for precision improvement in molecular dynamics simulation. [4+12]
7. Derive an expression for calculating thermodynamic quantities of a system in 6 N-dimensional phase space using Monte Carlo simulation. [16]
8. Describe the Monte Carlo simulation of phase equilibria. [16]


SET :4

1. What is central multipole expansion? How is it used to describe molecules?[4+12]
2. What are Vander Waals interactions? Describe briefly various types of Vander Waals interactions between atom. [6+10]
3. Explain in detail how
(a) heat capacity and
(b) pressure are calculated from molecular simulations. [8+8]
4. What is a block method in a molecular simulation program? Describe its use and importance in improving the molecular simulation programme. [4+12]
5. Describe very briefly any four integration methods used in molecular dynamics simulation of molecules with continuous potentials. [16]
6. What are holonomic and non-holonomic constraints? How they are used in simulation of flexible molecules? [8+8]
7. Explain the following :
(a) equilibrium phase
(b) production phase
(c) pseudo random numbers
(d) linear congruential method. [4+4+4+4]
8. Describe the ‘Widom approach’ in calculation of chemical potential. [16]