# LAMMPS Polymer

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In the Angle section listed the angles between atoms. First column is the angle number, second - angle ID, then comes the atom's number between which the angle is defined. Example of the distribution of the atoms can be seen on the picture to the left. | In the Angle section listed the angles between atoms. First column is the angle number, second - angle ID, then comes the atom's number between which the angle is defined. Example of the distribution of the atoms can be seen on the picture to the left. | ||

Dihedrals are a little bit more complicated. To define a diherdal four atoms are needed. Syntax are pretty much similar to the angles section. The only difference is that one more atom is needed to define a dihedral. Basically, the dihedral angle is the angle between the planes formed by 2 groups of 3 neighbor atoms. You see the example on the picture to the right. | Dihedrals are a little bit more complicated. To define a diherdal four atoms are needed. Syntax are pretty much similar to the angles section. The only difference is that one more atom is needed to define a dihedral. Basically, the dihedral angle is the angle between the planes formed by 2 groups of 3 neighbor atoms. You see the example on the picture to the right. | ||

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== LAMMPS Script == | == LAMMPS Script == |

## Revision as of 16:29, 30 November 2011

## Abstract

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

## Input File

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.

The data file is shown below and available for download here: https://icme.hpc.msstate.edu/mediawiki/images/e/e1/PE_cl100.txt

|# Model for PE 100 atoms 99 bonds 98 angles 97 dihedrals 1 atom types 1 bond types 1 angle types 1 dihedral types 0.0000 158.5000 xlo xhi 0.0000 158.5000 ylo yhi 0.0000 100.0000 zlo zhi Masses 1 14.02 Atoms 1 1 1 5.6240 5.3279 51.6059 2 1 1 7.4995 7.4810 50.2541 3 1 1 8.2322 8.0236 51.2149 4 1 1 9.6108 9.9075 51.7682 5 1 1 11.5481 11.3690 50.4167 6 1 1 12.9409 13.4562 50.2481 7 1 1 14.4708 14.8569 50.0868 8 1 1 16.1916 16.4790 50.5665 9 1 1 17.1338 17.6853 51.8189 10 1 1 19.1109 19.4000 50.3869 ... Bonds 1 1 1 2 2 1 2 3 3 1 3 4 4 1 4 5 5 1 5 6 6 1 6 7 7 1 7 8 8 1 8 9 9 1 9 10 10 1 10 11 ... Angles 1 1 1 2 3 2 1 2 3 4 3 1 3 4 5 4 1 4 5 6 5 1 5 6 7 6 1 6 7 8 7 1 7 8 9 8 1 8 9 10 ... Dihedrals 1 1 1 2 3 4 2 1 2 3 4 5 3 1 3 4 5 6 4 1 4 5 6 7 5 1 5 6 7 8 6 1 6 7 8 9 7 1 7 8 9 10

Here, the first section defines the numbers of atoms, bonds, angles and dihedrals. Lower you can see the types and the box sizes. Below that are the simulation box sizes.

Then comes the Atoms section. The first column is the atom number, then comes the atom type and some other information not used in this tutorial. Last three columns is the atom's x, y and z coordinates correspondingly.

In the Angle section listed the angles between atoms. First column is the angle number, second - angle ID, then comes the atom's number between which the angle is defined. Example of the distribution of the atoms can be seen on the picture to the left.
Dihedrals are a little bit more complicated. To define a diherdal four atoms are needed. Syntax are pretty much similar to the angles section. The only difference is that one more atom is needed to define a dihedral. Basically, the dihedral angle is the angle between the planes formed by 2 groups of 3 neighbor atoms. You see the example on the picture to the right.