Computer Simulation in Materials Science 1991
DOI: 10.1007/978-94-011-3546-7_7
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Cited by 71 publications
(68 citation statements)
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“…All bond lengths were constrained. All simulations were performed in the NPT ensemble at 298 K and 1 bar, using Berendsen weak-coupling algorithms (28). All details on the force fields are provided in SI Appendix.…”
Section: Methodsmentioning
confidence: 99%
“…All bond lengths were constrained. All simulations were performed in the NPT ensemble at 298 K and 1 bar, using Berendsen weak-coupling algorithms (28). All details on the force fields are provided in SI Appendix.…”
Section: Methodsmentioning
confidence: 99%
“…Non-bonded forces were cut off at 14 Å and electrostatics were treated by utilizing the Particle Mesh Ewald method (Kollman, 1992). For the NPT simulation, the Berendsen weak coupling method (Berendsen, 1991) was applied with coupling constants of 0.1 pseconds and 0.5 pseconds respectively, to maintain the system at 300K and 1 atm. Images of trajectory were recorded every 200 picoseconds.…”
Section: Structural Model Constructionmentioning
confidence: 99%
“…The equations of motion were solved using the leapfrog integration algorithm, with a time step of 1 fs. In the equilibration runs the Berendsen thermostat and barostat [30] (the latter only in NpT ensembles) was used, whereas in the production runs, temperature was controlled using the Nosé-Hoover thermostat [31] and pressure (in NpT ensemble) was controlled by the Parrinello--Rahman barostat [32]. For temperature control, coupling constants of 0.03 and 0.1 ps were used for Berendsen and Nosé-Hoover thermostats, respectively.…”
Section: Methodsmentioning
confidence: 99%