Whenever there exists a crossover from one potential to another, computational problems are introduced in Molecular Dynamics (MD) simulation. These problem are overcome here by an algorithm, described in detail. The algorithm is applied to a 2-body particle potential for a hysteresis loop reaction model. Extreme temperature conditions were applied to test for algorithm effectiveness by monitoring global energy, pressure and temperature discrepancies in an equilibrium system. No net rate of energy and other flows within experimental error should be observed, in addition to invariance of temperature and pressure along the MD cell for the said system. It is found that all these conditions are met only when the algorithm is applied. It is concluded that the method can easily be extended to Nonequilibrium MD (NEMD) simulations and to reactive systems with reversible, non-hysteresis loops.

The packages used extensively for biophysical simulations include CHARMM, GROMACS, DL_POLY, IMD, and AMBER [

For both synthetic and nonsynthetic methods using

The model reaction simulated may be written as

Potentials used for this work.

The above all refer to clearly defined spatial boundaries where there is a change of potential interaction type. In stochastic analysis [

The temperature

The velocity Verlet algorithm [

For a Hamiltonian

A virtual potential which scales velocities to preserve momentum and energy can be constructed about region

The external work done

Question (i) above leads to the following.

Relative to the velocities at any

From the

The above Inequality leads to a certain asymmetry concerning forward and backward reactions, even for reversible reactions where the regions of formation and breakdown of molecules are located in the same region with the reversal of the sign of approximate

Figure

Values for the mean heat supply per unit step and temperature. The error is one unit of standard error for the quantities.

Curve | Mean temperature | ||
---|---|---|---|

−.2274E+00 | −.2295E+00 | 0.9063E+01 | |

−.5602E+00 | −.5596E+00 | 0.1032E+02 | |

−.4161E−01 | −.4089E-01 | 0.8774E+01 | |

−.5201E−01 | −.5103E−01 | 0.8980E+01 | |

−.5312E−03 | −.3334E−03 | 0.8082E+01 | |

0.1311E−02 | 0.1147E−02 | 0.7731E+01 | |

−.6823E−03 | −.1507E−02 | 0.1216E+02 | |

0.7291E−02 | 0.6343E−02 | 0.1088E+02 | |

−.9348E−03 | −.3379E−02 | 0.1622E+02 | |

0.1918E−01 | 0.1938E−01 | 0.1329E+02 |

Temperature profile across the cell for different set conditions

Pressure profile across the cell for different runs. The conditions of the runs and the labeling of the curves are exactly as in Figure

The curve at

Without difficulty, one can easily construct a reversible system where

The author is grateful to University of Malaya for a Conference grant to present this algorithm as an Invited Speaker at the Fifth ICDSA (2007, Atlanta) which this communication briefly reviews.