Discrete molecular dynamics (DMD) has emerged as a simplification of traditional molecular dynamics (MD). DMD employs discrete step function potentials in place of the continuous potential used in traditional MD. As a result, the simulation engine solves the ballistic equations of motion for only those particles participating in a collision, instead of solving Newton’s equations of motion for e...

Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chlorid...

Advances in computational power have greatly facilitated the successful implementation of large-scale computer simulations of biological assemblies and complex condensed phases. Researchers have developed numerous simulation techniques, but many of these share, at their core, the so-called molecular dynamics (MD) paradigm to simulate such systems. (See the “Molecular Dynamics in a Nutshell” sid...

Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and ...

A new algorithm for calculating intermolecular pair forces in Molecular Dynamics (MD) simulations on a distributed parallel computer is presented. The Arbitrary Interacting Cells Algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh, which has been spatially decomposed into irregular portions for parallelisation. It is intended for ...

Both atomic force microscopy (AFM) experiments and molecular dynamics (MD) simulation are carried out to investigate atomic stick-slip friction by sliding a Pt tip on an Au substrate. Efforts are taken to match the conditions for AFM experiment and MD simulation as closely as possible. The results show that AFM and MD provide consistent energetic parameters, which suggests that MD simulations c...

The new Arbitrary Interacting Cells Algorithm (AICA) for calculating intermolecular pair forces for Molecular Dynamics (MD) on a distributed parallel computer is presented. AICA is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh, which has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid m...