Energy calculations cutoff approximation

For AMBER, BIO +, or OPLS (energy calculation of biomacromolecules) Choose Constant (for systems in a gas phase or in an explicit solvent) or Distance dependent (to approximate solvent effects in the absence of an explicit solvent) and set Scale factor for Dielectric permittivity ( 1.0 with the default of 1.0 being applicable to most systems). Select either Switched or Shifted for Cutoffs and set Electrostatic (the range is 0 to 1 use 0.5 for... 

Force field calculations often truncate the non bonded potential energy of a molecular system at some finite distance. Truncation (nonbonded cutoff) saves computing resources. Also, periodic boxes and boundary conditions require it. However, this approximation is too crude for some calculations. For example, a molecular dynamic simulation with an abruptly truncated potential produces anomalous and nonphysical behavior. One symptom is that the solute (for example, a protein) cools and the solvent (water) heats rapidly. The temperatures of system components then slowly converge until the system appears to be in equilibrium, but it is not. 

A very simple version of this approach was used in early applications. An alchemical charging calculation was done using a distance-based cutoff for electrostatic interactions, either with a finite or a periodic model. Then a cut-off correction equal to the Born free energy, Eq. (38), was added, with the spherical radius taken to be = R. This is a convenient but ill-defined approximation, because the system with a cutoff is not equivalent to a spherical charge of radius R. A more rigorous cutoff correction was derived recently that is applicable to sufficiently homogeneous systems [54] but appears to be impractical for macromolecules in solution. 

All calculations presented here are based on density-functional theory [37] (DFT) within the LDA and LSD approximations. The Kohn-Sham orbitals [38] are expanded in a plane wave (PW) basis set, with a kinetic energy cutoff of 70 Ry. The Ceperley-Alder expression for correlation and gradient corrections of the Becke-Perdew type are used [39]. We employ ah initio pseudopotentials, generated by use of the Troullier-Martins scheme [40], The coreradii used, in au, were 1.23 for the s, p atomic orbitals of carbon, 1.12 for s, p of N, 0.5 for the s of H, and 1.9, 2.0, 1.5, 1.97,... 

In order to calculate the band structure and the density of states (DOS) of periodic unit cells of a-rhombohedral boron (Fig. la) and of boron nanotubes (Fig. 3a), we applied the VASP package [27], an ab initio density functional code, using plane-waves basis sets and ultrasoft pseudopotentials. The electron-electron interaction was treated within the local density approximation (LDA) with the Geperley-Alder exchange-correlation functional [28]. The kinetic-energy cutoff used for the plane-wave expansion of... 

Plane-wave GGA density-functional calculations [58] and similar computational conditions as used in the study by Koudriachova et al. [136], in the present work a kinetic energy cutoff of 380 eV and a k-point spacing of 0.06 A-1. c From ref. [137], where a modification of the 6-31G basis set was used. d For studies of pure anatase employing local density approximation (LDA) DFT calculations, see e.g. ref. [138]. 

The relaxation of the structure in the KMC-DR method was done using an approach based on the density functional theory and linear combination of atomic orbitals implemented in the Siesta code [97]. The minimum basis set of localized numerical orbitals of Sankey type [98] was used for all atoms except silicon atoms near the interface, for which polarization functions were added to improve the description of the SiOx layer. The core electrons were replaced with norm-conserving Troullier-Martins pseudopotentials [99] (Zr atoms also include 4p electrons in the valence shell). Calculations were done in the local density approximation (LDA) of DFT. The grid in the real space for the calculation of matrix elements has an equivalent cutoff energy of 60 Ry. The standard diagonalization scheme with Pulay mixing was used to get a self-consistent solution. In the framework of the KMC-DR method, it is not necessary to perform an accurate optimization of the structure, since structure relaxation is performed many times. 

In the work of Edwards et al [36], which included interactions only to the third neighbor shell (approximately 4.4 A), the problem of energy instability for a 1000 K simulation did not arise the timestep was lO s at all temperatures. Since no analysis of the effects of timestep and cutoff was presented, it is difficult to determine the reasons for the differences in the behavior observed by Edwards et al and in the present study. Some possibilities are (a) They may have employed a minimum image approach for the periodic boundary conditions, whereas we have calculated both primaryprimary and primary-image interactions for each atom, (b) Their system was much larger than ours (2048 vs 256 atoms), (c) Edwards et al used the NVE ensemble for the production simulations, in contrast to our choice of the NPT ensemble. 

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