Sage-Tips

What is GROMACS used for?

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.

What does GROMACS mean?

GROningen MAchine for Chemical Simulation
GROMACS is an acronym for GROningen MAchine for Chemical. Simulation. This sounds strange for a software package, but the. name arises from a collaborative project of our group in the. Department of Chemistry at the University of Groningen, The.

What is molecular dynamics simulation used for?

Steered molecular dynamics (SMD) simulations, or force probe simulations, apply forces to a protein in order to manipulate its structure by pulling it along desired degrees of freedom. These experiments can be used to reveal structural changes in a protein at the atomic level.

How do you reference GROMACS?

when you publish your results….However, we prefer that you cite (some of) the GROMACS papers:

1. Bekker et al. (1993)
2. Berendsen et al. (1995)
3. Lindahl et al. (2001)
4. van der Spoel at al. (2005)
5. Hess et al. (2008)
6. Pronk et al. (2013)
7. Pall et al. (2015)
8. Abraham et al. (2015)

How do you source GROMACS?

Quick and dirty installation

1. Get the latest version of your C and C++ compilers.
2. Check that you have CMake version 2.8.
3. Get and unpack the latest version of the GROMACS tarball.
4. Make a separate build directory and change to it.
5. Run cmake with the path to the source as an argument.
6. Run make, make check, and make install.

How do I run simulation in GROMACS?

create a ‘topology’ file. convert a PDB protein structure into a GRO file, with the structure centered in a simulation box (unit cell)…Run GROMACS initial setup with the following parameters:

1. param-file.
2. “Water model”: SPC/E.
3. “Force field”: OPLS/AA.
4. “Ignore hydrogens”: No.
5. “Generate detailed log”: Yes.

How do you do MD simulation with GROMACS?

Tutorial: Molecular dynamics (MD) simulation using Gromacs

1. Preparing protein file. Remove the other chains and hetatoms including the water molecules (HOH) from the protein file.
2. Converting PDB to gmx and generating topology.
3. Defining box.
4. Solvating the protein.
5. Adding ions.
6. Energy minimization.
7. Equilibration.
8. Running MD.

How do you source Gromacs?

How do you reference Gromacs?

Why do we need molecular dynamics?

Molecular dynamics can be used to explore conformational space, and is often the method of choice for large molecules such as proteins. In molecular dynamics the energy surface is explored by solving Newton’s laws of motion for the system (see 4.25 Applications of Molecular Dynamics Simulations in Drug Design).