GROMACS (Groningen machine for chemical simulations) is a software kit for modeling of physicochemical processes in molecular dynamics.
It was developed by the team of German Berendsen that worked in the Biophysical Chemistry Department of the University of Groningen. Currently, the project is supported by the team of enthusiasts that includes professors from Uppsala University and Royal Institute of Technology.
The software kit is intended for the modeling of biological molecules (e.g. lipid or protein molecules), which have a lot of interconnections between the atoms. It provides the high speed of calculation for the unconsolidated interconnections. It’s considered one of the fastest tools in the market.
This kit is free and open-source software distributed under the GPL license.
You can also check the Gromacs Tutorial / Manual in order to get the understanding of the program. In order to make it, scroll this page a bit, and you will find it.
What is the purpose of Gromacs
If we are talking about the modeling of molecular or atomic structures, we can divide all existing methods into two main groups: quantum-mechanical methods and molecular dynamics methods. These two groups have significant differences.
Quantum-mechanical methods are based on quantum mechanics. All the calculations are made on the base of ‘precise’ quantum equations or on the base of average data that is used to increase the speed of calculations. It’s worth noting that these methods can be used to calculate chemical reactions, i. e. transformations between various substances with great precision.
By saying precision, we mean the values of the binding energy and their difference before and after reactions. In order to describe the precision of this method, I want to notice that in some cases the calculated value was more precise than the experimental one. Furthermore, new experiments only confirmed the results of quantum-mechanical calculations. However, these methods have a significant disadvantage, i.e. they require the highest level of computational performance (in the case with the basic computers, the time of calculation for a system with a thousand atoms will take an eternity).
Molecular dynamics is based on the classic Newtonian mechanics. In other words, all calculations are made in the traditional way, using simple equations. That is the biggest weakness of this method. In one hand, it gives an opportunity to model systems with millions of atoms. In another hand, such calculations are made only at the level of intermolecular interaction, while chemical reactions are left aside, unlike the quantum-mechanical methods, where all the aspects are taken into account.
Keep staying on this page and you will find examples of simulation processes and detailed Gromacs manuals.
Examples of using Gromacs
DNA in water:
Relaxation of water molecules:
Protein simulation over IMD:
Oxysterol pulled through lipid bilayer:
Water and 5-layer graphene system:
Stretching polyethylene glycol:
Polycaprolactone molecule in a pure water:
Simulation of self assembling peptide:
Below you can find the Gromacs Tutorial video that shows the most efficient and fast ways of the application usage. Take your chance, and go through these guides right away.
Watch this Gromacs tutorial to make your first simulation easy:
Here is one more nice Gromacs manual for beginners:
How to install Gromacs on a Linux:
Gromacs installation in Ubuntu:
Gromacs installation process in CentOS:
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