Configurational temperature control for atomic and molecular systems

The Journal of Chemical Physics
Karl P Travis, Carlos Braga

Abstract

A new configurational temperature thermostat suitable for molecules with holonomic constraints is derived. This thermostat has a simple set of motion equations, can generate the canonical ensemble in both position and momentum space, acts homogeneously through the spatial coordinates, and does not intrinsically violate the constraints. Our new configurational thermostat is closely related to the kinetic temperature Nosé-Hoover thermostat with feedback coupled to the position variables via a term proportional to the net molecular force. We validate the thermostat by comparing equilibrium static and dynamic quantities for a fluid of n-decane molecules under configurational and kinetic temperature control. Practical aspects concerning the implementation of the new thermostat in a MOLECULAR DYNAMICS code and the potential applications are discussed.

References

Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Nov 23, 2000·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·O G JeppsD J Evans
Nov 23, 2000·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·L Lue, D J Evans
Oct 15, 2005·The Journal of Chemical Physics·Carlos Braga, Karl P Travis
Mar 18, 2006·The Journal of Chemical Physics·Carlos Braga, Karl P Travis
May 5, 2007·The Journal of Chemical Physics·Wm G Hoover, Carol G Hoover

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Citations

Feb 12, 2014·The Journal of Chemical Physics·Sergio De LucaPeter J Daivis
May 17, 2013·The Journal of Chemical Physics·Dino CostaMauro Ferrario
Dec 18, 2013·The Journal of Chemical Physics·Søren Toxvaerd
Feb 18, 2014·The Journal of Chemical Physics·P K Patra, B Bhattacharya
Jul 2, 2010·The Journal of Chemical Physics·A A SamoletovM A J Chaplain
May 24, 2015·The Journal of Chemical Physics·Puneet Kumar Patra, Baidurya Bhattacharya
Oct 27, 2016·The Journal of Chemical Physics·Harro R Dittmar, Peter G Kusalik
Nov 4, 2017·Soft Matter·Xiaocheng ShangBenedict Leimkuhler
Apr 24, 2015·Physical Chemistry Chemical Physics : PCCP·Niall J English, Conor J Waldron
Apr 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·S PieprzykA C Brańka
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Benedict Leimkuhler
Jun 1, 2014·Physical Review Letters·Harro Dittmar, Peter G Kusalik
Jun 17, 2021·The Journal of Physical Chemistry. B·Patrick A BonnaudJun-Ichi Fujita

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Software Mentioned

LE
MOLECULAR DYNAMICS
MONTE CARLO

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