Motivation Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods...

Ab initio techniques based on density functional theory in the projector-augmented-wave implementation are used to calculate the free energy and a range of other thermodynamic properties of liquid iron at high pressures and temperatures relevant to the Earth’s core. The ab initio free energy is obtained by using thermodynamic integration to calculate the change of free energy on going from a si...

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l(max) on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole mo...

The ab initio atom-centered density matrix propagation (ADMP) and the quantum wavepacket ab initio molecular dynamics (QWAIMD) computational methods are briefly described. Studies on vibrational and electronic properties obtained utilizing these methods are highlighted. ∗ [email protected]

The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermolecular interaction parameters are obtained from preparative ab initio calculations on isolated molecules. The polarization energy in the EFP method is modeled with asymmetric anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbit...

A new force field has been customized for the variation of polynorbornene that contains a bicycloheptane group in the backbone structure. The force field was developed from ab initio density functional theory (DFT), and semiempirical electronic structure calculations for both stereochemical dimers of the 2,3 exoexo isomer of polynorbornene. The bond length and bond angle parameters were determi...

Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems. With the advent of ab-initio molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. Th...