Dear Nikhil, 

If you know the significance of  MD study for X-ray solved structures, then I will simply say all those points are applied to your question too. 

Dear Nikhil,

I found it to be appropriate to present a text taken from a review article entitled " Molecular Dynamics" which sheds light on the answer to your question:

Experiment plays a central role in science. It is the wealth of experimental results that provides a basis for the understanding of the chemical machinery of life. Experimental techniques, such as X-ray diffraction or nuclear magnetic resonance (NMR), allow determination of the structure and elucidation of the function of large molecules of biological interest. Yet, experiment is possible only in conjunction with models and theories. Computer simulations have altered the interplay between

experiment and theory. The essence of the simulation is the use of the computer to model a physical system. Calculations implied by a mathematical model are carried

out by the machine and the results are interpreted in terms of physical properties. Since computer simulation deals with models it may be classified as a theoretical method. On the other hand, physical quantities can (in a sense) be measured on a computer, justifying the term ‘computer experiment’. The crucial advantage of simulations is the ability to expand the horizon of the complexity that separates

‘solvable’ from ‘unsolvable’. Basic physical theories applicable to biologically important phenomena, such as quantum, classical and statistical mechanics, lead to equations that cannot be solved analytically (exactly), except for a few special cases. The quantum Schro¨dinger equation for any atom but hydrogen (or any molecule) or the classical Newton’s equations of motion for a system of more than two point masses can be solved only approximately. This is what physicists call the many-body problem. It is intuitively clear that less accurate approximations

become inevitable with growing complexity. We can compute a more accurate wave function for the hydrogen molecule than for large molecules such as porphyrins,

which occur at the active centres of many important biomolecules. It is also much harder to include explicitly the electrons in the model of a protein, rather than

representing the atoms as balls and the bonds as springs. The use of the computer makes less drastic approximations feasible. Thus, bridging experiment and theory by means of computer simulations makes possible testing and improving

our models using a more realistic representation of nature. It may also bring new insights into mechanisms and processes that are not directly accessible through experiment. On the more practical side, computer experiments can be

used to discover and design new molecules. Testing properties of a molecule using computer modelling is faster and less expensive than synthesizing and characterizing it in a real experiment. Drug design by computer is commonly used in the pharmaceutical industry.

http://dasher.wustl.edu/chem430/reading/md-intro-1.pdf

Hoping this will be helpful,

Rafik

Molecular modeling tools are idea generators. Nothing more; nothing less.