Molecular Simulations with Abalone

Abalone is designed for molecular-mechanical modeling on a Windows personal computer. The main direction is the modeling of polypeptides and small proteins in AMBER force fields. However, protein modeling is of limited value by itself. Most often it is necessary to model the interaction of proteins with other substances. Three features of Abalone facilitate such tasks:

  1. Abalone supports the AMBER-ii force field. AMBER-ii is an extension of AMBER03. A more accurate parametrization for the alkanes in it was done. A parametrization for perfluoroalkanes, nonmetals of the third and subsequent periods and parametrization for many metal ions has been introduced.
  2. Abalone interacts with the quantum chemical program with which we can calculate the parameters necessary for the modeling molecule is absent in the AMBER-ii.
  3. If any parameters are not defined, then Abalone assigns them default values (ad hoc mode). These parameters are partly borrowed from the DREIDING force field and have been defined for all elements. Of course this is a very simplified scheme. However, it is sufficient for some tasks, and most importantly it supports the model in working condition and allows to improve it incrementally. (To make sure that all parameters are explicitly defined in the model, you can turn off the ad hoc mode.)

Abalone is designed to be as portable as possible among Windows systems. In fact, the only requirement is the availability of OpenGL drivers (when starting from the command line under the script control even this is not necessary). Therefore, it is 32-bit and compiled in such a way that it works on any Windows since XP.

Methods of molecular dynamics and hybrid Monte Carlo benefit from the GPU acceleration on video cards supporting CUDA technology. If there is no corresponding video card on the computer, then Abalone is running on the CPU. The greatest CPU acceleration is achieved for water.





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