MOLECULAR SIMULATIONS

We know that each and every topic of research is very vast and full of challenges.
I wish to accomplish my project on "Molecular Simulations" and work for the following issues
giving emphasis on the first one.

A molecular simulation performs numerical experiments that enable one to obtain accurate
physicochemical data provided sampling and energy force field issues are addressed carefully.
Some of the Challenges we are facing are:

1. The difficulty of establishing the link between the macroscopic properties and their energetic
description or that of significant parameters at mesoscopic or molecular scale.

2. The sampling challenge: Smart methods must be developed to sample specific states of the model
system. It cannot be solely data-oriented, but also discovery-oriented. Molecular simulation is a
numerical experiment.
Consequently, the results are prone to systematic and statistical errors. The systematic errors must
be evaluated and then eliminated.

3. The potential energy is a function of the atomic positions (3N) of all the atoms in the system.
Due to the complicated nature of this function, there is no analytical solution to the equations of
motion, they must be solved numerically.

The algorithms should be designed carefully such that

It should conserve energy and momentum.
It should be computationally efficient
It should permit a long time step for integration.

4. There is no unifying equation such as Newton’s second law of motion in mechanics, Maxwell’s
equations in electrodynamics, and Schrödinger’s equation in nonrelativistic quantum mechanics.
"The concepts are universal, but their application to particular systems is not."

5. We cannot simulate a macroscopic system of 10^23 particles on a computer, keeping that in mind
we find that even small systems of the order of 100 particles are sufficient to illustrate the
qualitative behavior of macroscopic systems.

6. Another serious issue is Randomness. Many dynamical processes are modelled probabilistically.
For Example - State transitions in thermodynamics and between macroscopic partitions of classical
statistical mechanical systems.
Molecular dynamics simulations generate information at the microscopic level, including atomic
positions and velocities.
The conversion of this microscopic information to macroscopic observables such as pressure, energy,
heat capacities, etc. requires statistical mechanics.
The connection between microscopic simulations and macroscopic properties is made via statistical
mechanics which provides the rigorous mathematical expressions that relate macroscopic properties
to the distribution and motion of the atoms and molecules of the N-body system; molecular dynamics
simulations provide the means to solve the equation of motion of the particles and evaluate these
mathematical formulas. With molecular dynamics simulations, one can study both thermodynamic
properties and time dependent (kinetic) phenomenon.

The basic idea is that if one allows the system to evolve in time indefinitely, that system will
eventually pass through all possible states. One goal, therefore, of a molecular dynamics simulation is
to generate enough representative conformations such that this equality is satisfied. If this is the
case, experimentally relevant information concerning structural, dynamic and thermodynamic
properties may then be calculated using a feasible amount of computer resources. Because the
simulations are of fixed duration, one must be certain to sample a sufficient amount of phase space.

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