Algorithm and software to simulate molecular behavior

Bio Algos

Bio Algos

A molecule is a group of two or more atoms that are electronically neutral.  Those atoms are held together by chemical bonds. The molecules are generally very small in size and cannot be seen without microscope.    The molecules are treated with great importance in different disciplines of science.  Quantum physics, chemistry, biochemistry, organic chemistry are largely concerned and dependent of molecules and related applications.  Especially the contemporary biological sciences are making extensive use of molecules along its behavior in specific conditions for solving different issues related to biology.  Undersigning the behavior of molecules under different circumstances is very important for the respective science disciplines. For ease and convenience in observing the behaviors of molecules, different software is extensively used by the scientists and researchers. That software enables the scientists in studying molecules’ behavior in virtual environments with low cost.

The software used for understanding of molecular behavior generally work by simulating the behavior of molecules under predefined conditions.  Simulation means imitating the real-world situations or process or behavior over time. This simulating is generally implemented by using computers along with different algorithm and software. The researchers have to input the parameters representing the environment and based on that the software process relevant data and they display the result visually on the monitor. Computer aided simulation is now used in almost every discipline of sciences.

For understanding molecular behavior with simulation, dedicated software are available. Among those AMBER, CHARMm and GROMACS are most mentionable.


AMBER is particularly helpful for simulating of molecular behavior related to nucleic,     proteins and carbohydrates.  AMBER consists of three different kinds of programs. Preparation, simulation and analysis are performed by those programs. Therefore, interpretation of simulations results can also be made with AMBER. CHARMm is software for molecular simulations.  Avogadro is another software for the same purpose and available free of cost. The source code of this software package is also open to all.  There is much other software for molecular simulation and many of those are free and open sourced. 3D / 2D modeling of molecules can also be performed with that software.

The software uses different algorithms for performing the simulation of molecular.  Those algorithms can be divided into four main groups. They are:  integrators, Short-range interaction, Long-range interaction, Parallelization

. Depending upon the requirements and objectives,   researches choose the appropriate algorithm for using in simulations.  The concerned software also suggests the most appropriate algorithm, for a particular simulation, to the researchers.

Simulation software for understanding the behavior of molecules    allow the researchers and scientists to investigate critical problems with much ease and in a cost efficient way.

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