Molecular Modeling Tutorial

Computational modelling has gained an increasingly important role in biochemical and biomolecular sciences over the past decades. This is related to significant developments in terms of methodology and software, as well as the amazing technological advances in computational hardware, and fruitful connections across different disciplines. Virtual libraries of several million compounds searching for potential new inhibitors can be screened. Simulations of large biomolecular complexes can be run in micro or even millisecond timescales. Protein structures can be predicted with similar accuracy to high-resolution X-ray crystallography.

The appearance of a variety of standardised molecular modelling software packages, including GROMACS, Amber, CHARMM, GROMOS, and NAMD, has transformed the field of computational chemistry by commoditising molecular simulations and making it accessible to a broader group of researchers. All these packages have complementary strengths and profiles, with GROMACS and NAMD being two of the most popular. Considering GROMACS and NAMD as only MD engines there is no dramatic difference as to their performance, both work with a variety of force fields, and have GPU acceleration implemented. However, small differences should be mentioned, such as the possibility to perform QM/MM simulation in GROMACS, or NAMD's extensibility to user-written scripts. Both packages are distributed free of charge with source code. Moreover, for NAMD, there are downloadable binaries for a variety of platforms. This can be useful for a beginner in computational chemistry, as a compilation of MD software might not always be straightforward. Both GROMACS and NAMD are parallel molecular dynamics engines, designed for high-performance simulations of large biomolecular systems, with GROMACS being better for simulations of smaller systems on medium-size supercomputers. To achieve the best performance for a particular system on a particular supercomputer we recommend initial benchmarking.

Various pieces of software are used for the visualization and analysis of molecular dynamics trajectories, like Modeller Modeling, Swiss Model, etc. Among the most popular and freely accessible tools are molecular modeling programs VMD(visual molecular dynamics) and USCF Chimera. For more extensive assessment of trajectories, such as clustering or modifications of system topologies, AmberTools and, in particular, cpptraj is recommended. Here, a wide variety of tutorials are available in different application scenarios.

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