If the cutoff is too large, too many water molecules will unnecessarily be deleted. Finally, let us use the \textit{fix npt} to control the temperature, as well as the pressure by allowing the box size to be rescaled along the \textit{x} axis: {\normalsize \begin{verbatim} fix mynpt...
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changed the thermostat to Berendsen, that one controls the temperature very well, but similar system was published before with Nosé-Hoover. The paper cited uses npt, I have done so as well with the same results, but I have tried to reduce...
If the temperature of the particle is then “measured” using the kinetic energy and equipartition, then this effective mass is what should be used in the kinetic energy. However, if two or more particles are in close proximity the particle-fluid constraint on each particle can make them ...
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lindemann is a Python package to calculate the Lindemann index of Molecular Dynamics simulation trajectorys, as well as the progression of the Lindemann index per frame or per atom and frame of temperature ramps for phase transition analysis. ...