In this tutorial Molecular dynamics simulation in LAMMPS is used to show what happens to a polymer chain at a certain temperature after some time. Chain's movement is caused by a molecular forces between atoms in the chain and by temperature of the chain. This factors are modeled in LAMMPS in order to show the behavior of this polymer chain. The chain was previously prepared in MATLAB. It contains 100 atoms with bound between neighbor atoms. Duding the simulation, firstly, the chain was left for do deform freely under the molecular forces and a random atomic fluctuation due to the temperature. After that the chain was minimized to find it's minimal energy condition.
Author(s): Mark A. Tschopp, Dmitry I. Zhuk.
Corresponding Author: Mark Tschopp
The polymer chain of 100 atoms was specially prepared in MATLAB. The atom's Z coordinate does not varies much, all of them are within 2Å. The distance between atoms is about 1.5Å. Basically, the chain goes from left upper to right lower corner of the box. At the right you can see the picture of the initial condition of the chain.