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| Software | Key features | Simulation system | Reference |
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| GROMACS | GROMACS (Groningen MAchine for chemical simulation) is an efficient and versatile MD program with source code that is suited for the simulation of biological (macro) molecules in aqueous and membrane environments. The program can be run on single processors or parallel computer systems and is compatible with various force fields such as GROMOS, OPLS, AMBER, and ENCAD force fields. | Proteins, lipids, carbohydrate, nucleic acids | [71] |
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| AMBER | Amber is an extensively used biomolecular simulation program with an assembly of codes that are designed to work together. It is a collection of codes that are designed to work together and principally divided into three major step-system preparation (antechamber, LEaP programs), simulation (sander), and trajectory analysis (ptraj analysis program). | Proteins, nucleic acids, carbohydrates | [72] |
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| CHARMM | CHARMM (chemistry at HARvard molecular mechanics) is a widely used molecular simulation program that is primarily designed to study biological molecules such as proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands. The calculations are based on different energy functions (quantum mechanical-molecular mechanical force fields, all-atom classical potential energy functions) and models such as explicit solvent, implicit solvent, and membrane models. | Proteins, lipids, carbohydrates, nucleic acids | [73] |
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| NAMD | NAMD is a high-performance biomolecular simulation program that employs the prioritized message-driven execution capabilities of the charm++/converse parallel runtime system compatible with parallel supercomputers and workstation clusters. | Proteins, lipids, carbohydrates, nucleic acids, | [74] |
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| Desmond | Desmond is a powerful molecular dynamic simulation program designed by D. E. Shaw with considerable speed, accuracy, and scalability. It supports explicit solvent simulations with periodic boundary conditions and can be used to model explicit membrane systems under various conditions. | Proteins, lipids | https://www.schrodinger.com/desmond |
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| Tinker | Tinker is a molecular modeling and dynamic package written primarily in a standard Fortran 95 with OpenMP extensions. It supports a wide variety of classical molecular simulations particularly biomolecular calculations and offers various force fields including the modern polarizable atomic multipole-based AMOEBA model. | Proteins, nucleic acids | [75] |
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| LAMMPS | LAMMPS (large-scale atomic/molecular massively parallel simulator) is a classical molecular dynamic code for materials modeling. It has potentials for soft matter (biomolecules, polymers), solid-state materials (metals, semiconductors), and coarse-grained or mesoscopic systems. | Proteins, lipids, carbohydrates, nucleic acids | https://lammps.sandia.gov/ |
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| DL_POLY | DL_POLY is a general purpose molecular dynamic simulation package, which allows the study of liquids of large complexity. The code is developed using the replicated data (RD) parallelization strategy. | Membranes, proteins | [76] |
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