Software

Molecular Dynamics Simulation Programs

Programming is an essential component of the computational research. It helps in developing various tools and analysing the simulation trajectories. However, there are several classical molecular dynamics (MD) simulation software already available for the beginners. Using these tools, one can enter in the research field. Most of these tools are freely available for academic research.

• Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS):
  LAMMPS is C++ based parallel MD programs. It is very suitable for both atomistic and coarse-grained simulations. The calculations can be performed using both central processing units (CPUs) and graphics processing units (GPU) computer resources.
  Download link: https://lammps.sandia.gov/download.html

• GROMACS:
  GROMACS is also written in C/C++. It is very convenient for the simulations of biological systems such as proteins, lipids, membranes, nucleic acids. Like LAMMPS, it also support GPU calculations.
  Download link: http://www.gromacs.org/Downloads

• The DL_POLY Molecular Simulation Package:
  DL_POLY is Fortran90 based parallel MD programs. The parallelization is based on the static/equi-spatial Domain Decomposition (DD) model.
  Download link: https://www.scd.stfc.ac.uk/Pages/DL_POLY-Registration.aspx

• NAMD:
  NAMD is another Charm++ parallel objects based C++ MD software. It also supports GPU Acceleration and is useful for the simulations of biological systems.
  Download link: https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD

LAMMPS Input Builder

A generalized program, which uses OPLS-AA (Optimized Potentials for Liquid Simulations All Atom) force field will be shared soon!