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Lecture

Equilibrium GLE sampling

Description

This lecture covers Equilibrium Generalized Langevin Equation (GLE) sampling in atomistic modeling, focusing on optimizing sampling efficiency, custom-tailored thermostats, and canonical sampling GLE. The instructor discusses the concept of optimal sampling efficiency, the process of customizing thermostats, and the importance of canonical sampling for high statistical efficiency. The lecture emphasizes fine-tuning molecular dynamics (MD) sampling properties by adjusting GLE parameters and provides insights into pre-optimized parameter sets available online.

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Related concepts (32)

Sampling (statistics)

In statistics, quality assurance, and survey methodology, sampling is the selection of a subset or a statistical sample (termed sample for short) of individuals from within a statistical population to estimate characteristics of the whole population. Statisticians attempt to collect samples that are representative of the population. Sampling has lower costs and faster data collection compared to recording data from the entire population, and thus, it can provide insights in cases where it is infeasible to measure an entire population.

Molecular modelling

Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.

Simple random sample

In statistics, a simple random sample (or SRS) is a subset of individuals (a sample) chosen from a larger set (a population) in which a subset of individuals are chosen randomly, all with the same probability. It is a process of selecting a sample in a random way. In SRS, each subset of k individuals has the same probability of being chosen for the sample as any other subset of k individuals. A simple random sample is an unbiased sampling technique. Simple random sampling is a basic type of sampling and can be a component of other more complex sampling methods.

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.

Survey sampling

In statistics, survey sampling describes the process of selecting a sample of elements from a target population to conduct a survey. The term "survey" may refer to many different types or techniques of observation. In survey sampling it most often involves a questionnaire used to measure the characteristics and/or attitudes of people. Different ways of contacting members of a sample once they have been selected is the subject of survey data collection.

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