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The spin spiral ground state was then used as a starting configuration for all other finite magnetic field simulations.
These pinning points are comparable to those of the isolated Frank Read sources often used as a starting configuration in previous discrete dislocation dynamics simulations.
During the steered MD simulations the backbone atoms of the protein are held fixed and the atoms of the fullerene are held by a harmonic constraint of 0.2 kcal/mol/Å2 to maintain the root-mean-square deviation, with reference to a starting configuration below 0.25 Å so that no significant distortion takes place.
The final configuration of a 10 ns simulation was used as a starting configuration for the DSPC system with 50 mol% of cholesterol.
In the TOL, "the subject must construct a stack of objects from a starting configuration in series of individual moves" ([1], p. 203).
In a series of nine different problems, participants are asked to move a set of five disks from a starting configuration, which has three vertical pegs on top of a wooden platform.
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In the IMP modeling procedure we perform a large number of independent modelling runs, each starting from a random starting configuration and undergoing thousands of rounds of small random model perturbations, in order to achieve full sampling of conformational space.
This procedure was applied to reduce the bias from the individual peptide's starting position and configuration and to ensure a fully monomeric starting configuration for each of the conducted simulation runs, respectively.
ARES is managed via an easy-to-use interface that implements a centralized menu (Fig. 2a) for accessing the system of forms the user need to sequentially complete in order to introduce the starting configuration of a P-system scenario, run a simulation, and access the results.
For each problem, the beads have to be moved from the starting configuration to a target position in the minimum number of moves possible.
To further test the effects of the 3-D structure, and to demonstrate that more flux is transferred and more energization occurs when additional ballooning/interchange instability occurs, we have taken the fields in the y=0 plane from the 3-D simulation as the starting configuration for a 2-D MHD simulation, imposing the same resistivity.
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