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This prevents the simulation from adequately sampling both phases. Umbrella sampling is a means of "bridging the gap" in this situation. The standard Boltzmann weighting for Monte Carlo sampling is replaced by a potential chosen to cancel the influence of the energy barrier present. The Markov chain generated has a distribution given by
The match-to-sample task has been shown to be an effective tool to understand the impact of sleep deprivation on short-term memory. One research study [9] compared performance on a traditional sequential test battery with that on a synthetic work task requiring subjects to work concurrently on several tasks, testing subjects every three hours during 64 hrs of sleep deprivation.
Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology.It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape.
When examining a system computationally one may be interested in knowing how the free energy changes as a function of some inter- or intramolecular coordinate (such as the distance between two atoms or a torsional angle). The free energy surface along the chosen coordinate is referred to as the potential of mean force (PMF). If the system of ...
Let be the estimated variance, sometimes called the “sample” variance; it is the variance of the results obtained from a relatively small number of “sample” simulations. Choose a k {\displaystyle k} ; Driels and Shin observe that “ even for sample sizes an order of magnitude lower than the number required, the calculation of that ...
Situation sampling involves the study of behavior in many different locations, and under different circumstances and conditions. [2] By sampling different situations, researchers reduce the chance that the results they obtain will be particular to a certain set of circumstances or conditions.
Coding reliability [4] [2] approaches have the longest history and are often little different from qualitative content analysis. As the name suggests they prioritise the measurement of coding reliability through the use of structured and fixed code books, the use of multiple coders who work independently to apply the code book to the data, the measurement of inter-rater reliability or inter ...
PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. It is designed to be used together with ACEMD, AMBER, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum ESPRESSO, but it can also be used together with analysis and visualization tools VMD, HTMD, and ...