Manikumar Athan You could use GROMACS or NAMD to do molecular dynamics (MD) simulations on ligand-protein complexes. Both of these programs are free.

• Thank you for making this recommendation, Professor Rudy J Richardson

Desmond is also free for academic use.

If you think you are comfortable with command-line use, you can use GROMACS, and if you think that you are comfortable with GUI, go for the Desmond. GROMACS and Desmond have their own pros and cons, GROMACS gives more control and more customization options, like calculation of free binding energy, etc after the simulation, while at the same time, is somewhat difficult for analysis of results if compared with Desmond. Desmond, on the other hand is relatively easier than GROMACS and provide full report of analysis in GUI and pdf, but is less customizable (fixed OPLS force field) and does not allow free energy calculations in free academic license.

Hi, you can also try AMBER, it has recently become free for academic use. It has a lot of tutorials and it is really fast on GPUs.

For GUI I highly recommend CHARMM-GUI (https://www.charmm-gui.org/) or VMD (https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD , especially if you use NAMD).

GUI for Desmond is incorporated in Schrodinger Suites and works only with a valid Schrodinger license, although Desmond itself is available for academic use.

GROMACS for LINUX and NAMD for window

Several free software packages are available for Molecular Dynamics (MD) simulations, each with different features and capabilities.

1. GROMACS

• Platform: Linux, macOS, Windows
• Description: GROMACS is one of the most widely used MD packages due to its high performance, especially for simulations of biomolecules. It is open-source and includes a wide range of tools for pre- and post-processing of simulation data.
• Website: GROMACS

2. LAMMPS

• Platform: Linux, macOS, Windows
• Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is highly flexible and scalable, suitable for simulating a wide variety of materials and systems. It supports parallel computing and can handle large-scale systems.
• Website: LAMMPS

3. NAMD

• Platform: Linux, macOS, Windows
• Description: NAMD is designed for high-performance simulations of large biomolecular systems. It is known for its efficiency in parallel computing environments and is often used in conjunction with the visualization tool VMD (Visual Molecular Dynamics).
• Website: NAMD

4. AMBER (AmberTools)

• Platform: Linux, macOS
• Description: AmberTools is a suite of programs for preparing input files, analyzing simulations, and performing various other tasks related to MD. It includes a free version of the sander module for small-scale MD simulations.
• Website: AMBER

5. OpenMM

• Platform: Linux, macOS, Windows
• Description: OpenMM is a flexible library for MD simulations that can be used as a stand-alone application or as a library to add MD capabilities to other software. It’s particularly optimized for running on GPUs.
• Website: OpenMM

6. HOOMD-blue

• Platform: Linux, macOS, Windows
• Description: HOOMD-blue is designed for executing particle-based simulations on GPUs. It is efficient for systems with complex interactions and is widely used in soft matter research.
• Website: HOOMD-blue

7. CP2K

• Platform: Linux, macOS
• Description: CP2K is a program to perform molecular dynamics, quantum chemistry, and solid-state physics simulations. It is suitable for a wide range of simulations, including classical MD, ab-initio MD, and hybrid methods.
• Website: CP2K

These tools cover a broad range of MD applications, from biomolecular simulations to materials science.

Sergio Grunbaum : Excellent comprehensive summary!