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Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules
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10.1063/1.1906216
/content/aip/journal/jcp/122/22/10.1063/1.1906216
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/22/10.1063/1.1906216

Figures

Image of FIG. 1.
FIG. 1.

(a) The deviation of the energy from its mean value for the system of Gay–Berne particles plotted vs MD steps using Fincham (Ref. 27) (for a time step of ) and (b) time reversible and sympletic and time-reversible algorithms (for a time step of ).

Image of FIG. 2.
FIG. 2.

(a) The trajectory of the energy of the system of Gay–Berne particles using the time-reversible integrator for the rotation motion in the ensemble and (b) ensemble (isotropic cell fluctuation method) using a time step of .

Image of FIG. 3.
FIG. 3.

The trajectories (a) of the simulation box sides, (b) of the simulation box angles, (c) of the diagonal components of the pressure tensor, and (d) of the temperature of the system of Gay–Berne particles using the time-reversible integrator for the rotation motion of Miller et al. (Ref. 17) in the ensemble using the variable box shape method with a time step of .

Image of FIG. 4.
FIG. 4.

(a) Density and (b) order parameter as a function of the pressure at fixed temperature of in the molecular dynamics and Monte Carlo (Ref. 40) simulation results for 500 and 256 rodlike GB particles, respectively.

Image of FIG. 5.
FIG. 5.

(a) Radial pair distribution function , (b) parallel pair distribution function , (c) transverse pair distribution function , and (d) in-plane bond orientational correlation function as determined by MD simulations in the ensemble at reduced temperature of using the fixed aspect ratio method.

Image of FIG. 6.
FIG. 6.

(a) Radial pair distribution function , (b) parallel pair distribution function , and (c) transverse pair distribution function as determined by MD simulations in the ensemble at reduced temperature of and and 8.0 using the shape-varying cell method.

Image of FIG. 7.
FIG. 7.

(a) and (b) Snapshots for the nematic and smectic phases using the fixed aspect ratio method, and (c) and (d) the snapshots for the nematic and smectic phases using the variable shape box method in the MD simulations at .

Tables

Generic image for table
Table I.

The values of the parameters involved in the Yoshida–Suzuki multiple time steps integrators (Refs. 18, 37, and 38).

Generic image for table
Table II.

The percentage relative drift and the standard energy error in constant , and ensembles for Fincham algorithm (Ref. 27), time reversible algorithm according to Matubayasi and Nakahara (Ref. 16), and time reversible and/or symplectic algorithm according to Miller et al. (Ref. 17) time step.

Generic image for table
Table III.

The percentage relative drift and the standard energy error of the total extended energy as a function of the thermostating rates in constant ensemble and the number of the inner steps used in the integration of the chain thermostats variables as proposed by Martyna et al. (Ref. 18). The values of the temperature are also reported together with their standard deviations. The time step was fixed to .

Generic image for table
Table IV.

The percentage relative drift and the standard energy error of the total extended energy vs the thermostating and barostating rates in the ensemble (isotropic cell fluctuations). The values of the pressure and temperature are also reported together with their standard deviations. The time step was fixed to .

Generic image for table
Table V.

The percentage relative drift and the standard energy error of the total extended energy vs the thermostating and barostating rates in the ensemble (shape-varying cell fluctuations). The pressure tensor , pressure , and temperature are also reported together with their standard deviations. The time step was fixed to .

Generic image for table
Table VI.

MD simulation in the ensemble using fixed aspect ratio simulation method at the temperature . Results of the MC simulations are also presented as reported in Ref. 40.

Generic image for table
Table VII.

MD simulation in the ensemble using shape-varying cell simulation method at the temperature .

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/content/aip/journal/jcp/122/22/10.1063/1.1906216
2005-06-15
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/22/10.1063/1.1906216
10.1063/1.1906216
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