How do I install OpenMM?

How do I install OpenMM?

There are two ways to install OpenMM: using the Conda package manager (http://conda.pydata.org), or with standalone installers. (A third option is to compile it from source, which is discussed in Chapter 9.) Using Conda is the easier method, and is recommended for most users.

Where is OpenMM installed?

OpenMM is installed using the Conda package manager (https://docs.conda.io). Conda is included as part of the Anaconda Python distribution, which you can download from https://docs.continuum.io/anaconda/install.

Is OpenMM open source?

OpenMM is a high performance toolkit for molecular simulation. Use it as a library, or as an application. We include extensive language bindings for Python, C, C++, and even Fortran. The code is open source and actively maintained on Github, licensed under MIT and LGPL.

What is Gromacs package?

GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs).

What is Charmm force field?

Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them.

What can GROMACS do?

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported.

Who uses GROMACS?

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological …

How do I use Packmol?

The quick three steps

1. Get the pdb/xyz/mol2 files for each component of your system.
2. Get a suitable packmol script.
3. Run the script using the command: ./packmol < mixture.txt.

What is CHARMM used for?

The CHARMM program allows for generating and analysing a wide range of molecular simulations. The most basic kinds of simulation are minimizing a given structure and production runs of a molecular dynamics trajectory.

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.

Is GROMACS software free?

GROMACS is free software distributed under LGPLv2. 1, which even allows linking into commercial applications.