Table of Contents
What is LAMMPS stand for?
LAMMPS is a large scale classical molecular dynamics code, and stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers), solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems.
How do I create a LAMMPS data file?
Click Create Data File:
- The tool will identify the atom types in the structure according to the force field and the bonded parameters such as bonds, angles and dihedrals: types and coefficients for the energy expression used in the force field.
- Non-bonded parameters will be also included in the data file.
How do I use Packmol?
The quick three steps
- Get the pdb/xyz/mol2 files for each component of your system.
- Get a suitable packmol script.
- Run the script using the command: ./packmol < mixture.txt.
What language is LAMMPS?
C++
LAMMPS
| Original author(s) | Steve Plimpton, Aidan Thompson, Stan Moore, Axel Kohlmeyer, Richard Berger |
|---|---|
| Repository | github.com/lammps/lammps |
| Written in | C++ |
| Operating system | Cross-platform: Linux, macOS, Windows, FreeBSD |
| Platform | x86, x86-64 |
How do I restart Lammps?
Restart files are written on timesteps that are a multiple of N but not on the first timestep of a run or minimization. You can use the write_restart command to write a restart file before a run begins. A restart file is not written on the last timestep of a run unless it is a multiple of N.
What is Charmm GUI?
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM.
How do you cite Packmol?
Martínez, R. Andrade, E. G. Birgin, J. M. Martínez. Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13):2157-2164, 2009.