Simulations long-range truncation

Methods. To explore the effects of long range truncation on molecular dynamics simulations of proteins, a series of simulations have been performed. The two main questions which have been addressed are ... 

A final point to remember is that the simulation with the smallest deviation from the X-ray structure (0.25 angstrom switch) is probably the least realistic of the entire set of simulations that were truncated near 7.5 angstroms, which implies that a simulation should not be judged by this value alone. It is hoped that from these simulations that better methods for handling the truncation of long range potentials can become more universal. 

D. M. York, T. A. Darden, and L. G. Pedersen, The effect of long-range electrostatic interactions in simulations of macromolecular crystals - a comparison of the Ewald and truncated list methods, J. Chem. Phys., 99 (1993), 8345-8348. 

It is known that the method used to truncate the interatomic interactions can have an important effect. It has been demonstrated that the dielectric properties of simulated water are a sensitive function of the extent to which the long-range electrostatic interactions are included [40]. Simulations of phospholipid membrane-water systems showed that the behavior of the water near the membrane is incorrectly described if the electrostatic interactions are truncated at too short a distance, and hot water/cold-protein behavior is observed [10]. Given the importance of the potential/force truncation, we have investigated this issue for the copper system being simulated. This has been done in terms of the same properties as were used in examining convergence. 

The results outlined above for the RPM and the CHD fluid clearly show a discrepancy between MFFSS analyses (which are consistent with Ising-like criticality) and calculations of Cy in NVT MC simulations. To investigate this discrepancy, we have studied a class of fluids defined by the potential in Eq. (5) with a = 6 (which should give rise to Ising-like criticality since a > 4.7) and a = 4 and a = 3.1 (which are classical since a < 4.5). All simulations reported in this section were carried out in cubic simulation cells of side L. The potentials were truncated at L/2, and a long-range correction was calculated... 

In modem simulations, various Ewald summation methods are often used in order to correctly describe the long-range electrostatic interactions. The TIPwP potentials were originally parameterised using truncated Coulomb interactions and using these models with Ewald summation results in changes in both the thermodynamic and kinetic properties. 

---