In molecular dynamics (MD) simulations, a proper definition of kinetic energy is essential for controlling pressure as well as temperature in the isothermal-isobaric condition. The virial theorem provides an equation that connects the average kinetic energy with the product of particle coordinate and force. In this paper, we show that the theorem is satisfied in MD simulations with a larger time step and holonomic constraints of bonds, only when a proper definition of kinetic energy is used. We provide a novel definition of kinetic energy, which is calculated from velocities at the half-time steps (t − Δt/2 and t + Δt/2) in the velocity Verlet integration method. MD simulations of a 1,2-dispalmitoyl-sn-phosphatidylcholine (DPPC) lipid bilayer and a water box using the kinetic energy definition could reproduce the physical properties in the isothermal-isobaric condition properly. We also develop a multiple time step (MTS) integration scheme with the kinetic energy definition. MD simulations with the MTS integration for the DPPC and water box systems provided the same quantities as the velocity Verlet integration method, even when the thermostat and barostat are updated less frequently.
Skip Nav Destination
CHORUS
Article navigation
28 April 2018
Research Article|
April 26 2018
Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation
Jaewoon Jung
;
Jaewoon Jung
1
Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research
, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
2
Computational Biophysics Research Team, RIKEN Center for Computational Science
, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
Search for other works by this author on:
Chigusa Kobayashi;
Chigusa Kobayashi
2
Computational Biophysics Research Team, RIKEN Center for Computational Science
, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
Search for other works by this author on:
Yuji Sugita
Yuji Sugita
a)
1
Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research
, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
2
Computational Biophysics Research Team, RIKEN Center for Computational Science
, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
3
Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research
, 6-7-1 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
a)Author to whom correspondence should be addressed: sugita@riken.jp. Tel.: +81-48-462-1407. Fax: +81-48-467-4532.
Search for other works by this author on:
a)Author to whom correspondence should be addressed: sugita@riken.jp. Tel.: +81-48-462-1407. Fax: +81-48-467-4532.
J. Chem. Phys. 148, 164109 (2018)
Article history
Received:
October 06 2017
Accepted:
April 10 2018
Citation
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita; Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. J. Chem. Phys. 28 April 2018; 148 (16): 164109. https://doi.org/10.1063/1.5008438
Download citation file:
Sign in
Don't already have an account? Register
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Could not validate captcha. Please try again.
Sign in via your Institution
Sign in via your InstitutionPay-Per-View Access
$40.00
Citing articles via
Related Content
Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration
J. Chem. Phys. (September 2001)
Qualitative study of the symplectic Störmer–Verlet integrator
J. Chem. Phys. (June 1995)
A magnetic velocity Verlet method
Am. J. Phys. (December 2020)
Modeling of diatomic molecule using the Morse potential and the Verlet algorithm
AIP Conference Proceedings (March 2016)
Stability of velocity-Verlet- and Liouville-operator-derived algorithms to integrate non-Hamiltonian systems
J. Chem. Phys. (October 2018)