Molecular dynamics test particle method

Moller, D. Fischer, J., Vapour liquid equilibrium of a pure fluid from test particle method in combination with npt molecular dynamics simulations, Mol. Phys. 1990, 69, 463 173... 

Just as one may wish to specify the temperature in a molecular dynamics simulation, so it may be desired to maintain the system at a constant pressure. This enables the behaviour of the system to be explored as a function of the pressure, enabling one to study phenomena such as the onset of pressure-induced phase transitions. Many experimental measurements are made under conditions of constant temperature and pressure, and so simulations in the isothermal-isobaric ensemble are most directly relevant to experimental data. Certain structural rearrangements may be achieved more easily in an isobaric simulation than in a simulation at constant volume. Constant pressure conditions may also be important when the number of particles in the system changes (as in some of the test particle methods for calculating free energies and chemical potentials see Section 8.9). 

Moving beyond standard DNA and RNA duplexes, simulations of chemically modified DNA provide a further test of the simulation methods. To this end, we performed unrestrained molecular dynamics simulations on a standard d(CGCGAATTCGCG)2 dodecamer duplex in aqueous solution and its phosphoramidate (N3 -P) analog using the particle mesh Ewald summation technique (5) and recent AMBER force field (10). In the modified dodecamer each phosphodiester has been replaced by a phosphoramidate unit with a N3-P5 intemucleoside linkage. 

Gas solubiUties can also be determined by molecular dynamics simulations, using the Widom test particle insertion method to calculate the excess chemical potential fiex. or free energy of the penetrant molecules. The solubility can be obtained using Henry s law. If E is the interaction energy of a virtual penetrant molecule with the polymer inserted at random within the sample (the molecule is invisible to the polymer) then... 

The Zimm model apphes to dilute solutions, and, therefore, to the dynamics of a single solvated chain. It has become a benchmark system, used to test the validity of mesoscopic simulation methods. A single chain, modeled by bead-spring interactions, coupled to a surrounding solvent to account for hydrodynamic interactions, has been successfully simulated via (1) Molecular Dynamics [180-182], (2) Dissipative Particle Dynamics [183,184], Multi-Particle Collision Dynamics [185,186],... 

---