LAMMPS Examples

LAMMPS, or Large-scale Atomic/Molecular Massively Parallel Simulator, is a molecular dynamics simulator. It computes using the solution using spatial-decomposition techniques and hence is able to parallelize well across multiple processors.

LAMMPS Basic Example

This example is a simulation of a rhodopsin protein in a solvated lipid bilayer.

Post processing visualization of results

Post processing visualization of results


Import Job Setup Get Job Results


Simulation Code r13864
Analysis Type Molecular dynamics
Description All-atom rhodopsin protein in solvated lipid bilayer with CHARMM force field, long-range Coulombics via PPPM (particle-particle particle mesh), SHAKE constraints.
Suggested Hardware Nickel / 1 cores
Command
lammps -in in.rhodo
Estimated Run Time 23 minutes


LAMMPS Polymer Example

This is an example of molecular dynamics analysis with LAMMPS and post processing visualization on Rescale.

Post processing visualization of results (using Atom Eye)

Post processing visualization of results (using Atom Eye)


Import Job Setup Get Job Results


Simulation Code LAMMPS Aug 2015 (r13864)
Analysis Type Molecular dynamics
Description A 100 atoms polymer chain is put in a fixed temperature environment. The thermal energy of the environment randomly jiggles the polymer chain while the molecular bonds between the atoms are trying to hold the chain together. As the simulation goes on, the polymer chain is expected to evolve toward the same entropy state as its surrounding environment.
Suggested Hardware Nickel / 1 cores
Command
lammps -in in.deform.polychain.txt
Estimated Run Time 4 minutes