Berendsen barostat: Difference between revisions

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(New page: ==References== #[http://dx.doi.org/10.1063/1.448118 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak "Molecular dynamics with coupling to an external...)
 
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The '''Berendsen barostat''' <ref>[http://dx.doi.org/10.1063/1.448118    H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak "Molecular dynamics with coupling to an external bath", Journal of Chemical Physics '''81''' pp. 3684-3690 (1984)]</ref> is a method for controlling the [[pressure]] in a [[molecular dynamics]] simulation.
The Berendsen [[barostats | barostat]] adds an extra term to to the equations of motion which effects the pressure change (Eq. 12):
:<math>\left. \frac{dP}{dt} \right\vert_{\mathrm {bath} }  = \frac{P_0 - P}{\tau_P}</math>
where <math>P_0</math> is the reference pressure, i.e. the pressure of the external pressure "bath", and <math>P</math> is the instantaneous pressure.
<math>\tau_P</math> is a time constant.
Within this scheme the coordinates and the box sides are rescaled every step. Assuming the system is isotropic and within a cubic box the scaling factor <math>\mu</math> is given by (Eq. 20):
:<math> \mu = 1 - \frac{\kappa_T \Delta t}{3\tau_P} (P_0 -P)</math>
where <math>\kappa_T</math> is the [[Compressibility#Isothermal compressibility | isothermal compressibility]]. The value of <math>\kappa_T</math> only has to be reasonable; for example, both [[DL POLY]] and [[GROMACS]] use the value of the compressibility of [[water]] (at 1 atm and 300K, leading to
<math>\kappa_T = 4.6 \times 10^{-5} \mathrm{bar}^{-1}</math>).
==References==
==References==
#[http://dx.doi.org/10.1063/1.448118    H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak "Molecular dynamics with coupling to an external bath", Journal of Chemical Physics '''81''' pp. 3684-3690 (1984)]
<references/>
[[category: molecular dynamics]]
[[category: molecular dynamics]]

Latest revision as of 13:15, 24 January 2014

The Berendsen barostat [1] is a method for controlling the pressure in a molecular dynamics simulation. The Berendsen barostat adds an extra term to to the equations of motion which effects the pressure change (Eq. 12):

where is the reference pressure, i.e. the pressure of the external pressure "bath", and is the instantaneous pressure. is a time constant. Within this scheme the coordinates and the box sides are rescaled every step. Assuming the system is isotropic and within a cubic box the scaling factor is given by (Eq. 20):

where is the isothermal compressibility. The value of only has to be reasonable; for example, both DL POLY and GROMACS use the value of the compressibility of water (at 1 atm and 300K, leading to ).

References[edit]