Interesting question. InsyAllah I will explain in detail soon

Hi,

I have done simulation with MD in my M.Sc thesis. I have used Tinker to do explicit atomic simulation. In order to make input files, I have utilized HyperChem which is a powerful software to construct molecules with all details and calculating their properties and rules like Entropy.

Molden can create tinker input file with the MM3 force field. Quite practical to get the structure of the file, free to you to edit the atom type column if you want to change force field.

There are a large number of input files available, see:

http://dasher.wustl.edu/tinker/distribution/example/

http://dasher.wustl.edu/tinker/distribution/test/

These references can also help:

http://pubs.acs.org/doi/full/10.1021/ct200304d

http://pubs.acs.org/doi/full/10.1021/ct4003702

http://chembytes.wikidot.com/tnk-tut00

http://simtk.org/home/openmm