Self-guided molecular dynamics simulation for efficient conformational search

Article Abstract:

A novel molecular dynamics (MD) simulation method, also known as the self-guided MD simulation model, is aimed at dramatically improving the conformational searching efficiency. It is based on a new equation of motion wherein a guiding force is introduced to speed up the systematic motion. Comparative simulations of two peptide systems, an alanine dipeptide and a 16-residue synthetic peptide, were performed to investigate the improvement of the overall conformational searching efficiency and the possible changes of ensemble properties as well as the conformational distribution of the system. It is shown that the self-guided MD simulation model improved conformational searching efficiency but did not significantly alter the ensemble average properties and the conformational distributions of the systems.

Models, Conformational analysis

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Optimization of hydrocarbon chain interaction parameters: application to the simulation of fluid phase lipid bilayers

Article Abstract:

Molecular dynamics simulations of n-hexane, n-decane, n-pentadecane and 5-decene were conducted to find an optimal set of parameters for nonbonded interactions between atoms on different molecules. A set of 6-12 parameters for nonbonded interactions between methyls and methylenes on various molecules for which MD simulations generate densities and heats of vaporization for the n-alkanes that are in good agreement with experiment for n = 6, 10 and 15.

Analysis, Usage, Simulation methods, Simulation, Hydrocarbons

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