Molecular Simulations

Examples

Our programs are intended for molecular simulations. In many respects, they are similar to other packages of this kind but have some properties reflecting our specific interests and vision of the problem.

The main application is the modeling of biomolecules, in particular, proteins, lipids, and nucleic acids. Modeling over as long time periods as possible is desirable. The long-term simulations of biomolecules are the top priority for us. Other problems, e.g., simulating very large systems, are clearly of high importance but have lower priority in our terms. The point is that the modeling methods form a hierarchical system. The larger is the modeled system, the longer simulations it requires. Accordingly, large systems cannot be simulated to the accuracy achievable for small ones. Very large systems should be simulated using cruder methods on the indispensable condition of their calibration by accurate methods. That is why supporting the hierarchy of methods of different accuracy is the second priority. We believe that reaching the highest possible rate and accuracy for typical tasks using each method is more important than modeling the largest possible models at each level of method hierarchy. In particular, this standpoint suggests splitting large molecules into small fragments and applying as accurate quantum chemical methods as possible rather than calculating large molecules as a whole using crude methods. Of course, this is not unquestionable, and each case should be considered individually. However, this trend governs our choice of a particular set of methods.

The main attention is given to molecular mechanics modeling. The reference methods (and the main force fields) are AMBER and OPLS. We presume that the key to their success is an appropriate calibration with both quantum chemical methods and experimental data. These calibrations include not an eclectic set of all available data but rather a specific set of methods, which makes them systemically applicable to new molecules. For instance, using quantum mechanics to parameterize the torsion and electrostatic parameters or simulation of liquids to elaborate the van der Waals parameters seem justified. Accordingly, the package is to a considerable extent oriented to low molecular weight liquids, although its main task is the simulation of macromolecules.

The package is designed for routine tasks. As a result, the third priority is molecular graphics and various interactive methods of molecular model construction.

 

 

 

 

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