A novel method for molecular dynamics simulation in the isothermal-isobaric ensemble

TY - JOUR

T1 - A novel method for molecular dynamics simulation in the isothermal-isobaric ensemble

AU - Huang, Cunkui

AU - Li, Chunli

AU - Choi, Phillip Y.K.

AU - Nandakumar, K.

AU - Kostiuk, Larry W.

N1 - Funding Information: The financial support from NSERC for the authors (PC, KN and LWK) is gratefully acknowledged. CH acknowleges the financial support from the Ph.D. Scholarship of the University at Alberta and the Postgraduate Scholarship from NSERC.

PY - 2011/1/20

Y1 - 2011/1/20

N2 - A novel algorithm is proposed to study fluid properties in the isothermal-isobaric (NPT) ensemble. The major feature of this approach is that the constant pressure in the NPT ensemble is created by two auto-adjusting boundaries that allow the system volume to fluctuate. Relative to other methods used to create the NPT ensemble, this approach is simpler to perform since no additional variables are introduced into the simulation system. To test this method, two systems with the same constant target pressure and temperature but different thermostats (Nose-Hoover and Berendsen) were performed by using a commonly used cut-off distance (i.e. rc =2.5σ). The simulation results show that the proposed method works well in terms of creating spatially uniform mean temperature, pressure and density while still allowing ppropriate levels of instantaneous fluctuations for observable quantities. The fluctuations of the system volume produced by this method were compared with that calculated by the theoretical equation. To test the reliability of the proposed method, additional simulations were carried out at eight different thermodynamic states but with the use of a longer cut-off distance (rc = 4.5σ). The results were compared with those obtained using the Nose-Hoover barostat with an rc of 4.5σ, as well as with experiments. The comparison shows that the results using the algorithm proposed in this article agree well with those obtained using other methods.

AB - A novel algorithm is proposed to study fluid properties in the isothermal-isobaric (NPT) ensemble. The major feature of this approach is that the constant pressure in the NPT ensemble is created by two auto-adjusting boundaries that allow the system volume to fluctuate. Relative to other methods used to create the NPT ensemble, this approach is simpler to perform since no additional variables are introduced into the simulation system. To test this method, two systems with the same constant target pressure and temperature but different thermostats (Nose-Hoover and Berendsen) were performed by using a commonly used cut-off distance (i.e. rc =2.5σ). The simulation results show that the proposed method works well in terms of creating spatially uniform mean temperature, pressure and density while still allowing ppropriate levels of instantaneous fluctuations for observable quantities. The fluctuations of the system volume produced by this method were compared with that calculated by the theoretical equation. To test the reliability of the proposed method, additional simulations were carried out at eight different thermodynamic states but with the use of a longer cut-off distance (rc = 4.5σ). The results were compared with those obtained using the Nose-Hoover barostat with an rc of 4.5σ, as well as with experiments. The comparison shows that the results using the algorithm proposed in this article agree well with those obtained using other methods.

KW - isothermal-isobaric ensemble

KW - molecular simulation

KW - statistical mechanics

UR - http://www.scopus.com/inward/record.url?scp=79551702040&partnerID=8YFLogxK

U2 - 10.1080/00268976.2010.513345

DO - 10.1080/00268976.2010.513345

M3 - 文章

AN - SCOPUS:79551702040

SN - 0026-8976

VL - 109

SP - 191

EP - 202

JO - Molecular Physics

JF - Molecular Physics

IS - 2

ER -