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On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm
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10.1063/1.2779878
/content/aip/journal/jcp/127/18/10.1063/1.2779878
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/18/10.1063/1.2779878

Figures

Image of FIG. 1.
FIG. 1.

Error of estimators for an harmonic oscillator with force constant , , , and . Thick line, [Eq. (35)]; dashed line, [Eq. (36)]; dash-dotted line, [Eq. (38)]; and thin line, [Eq. (37)].

Image of FIG. 2.
FIG. 2.

Error of kinetic energy estimators for a collision of two Lennard-Jones particles, water oxygens with energy for , with . Thick line, [Eq. (35)]; dashed line, [Eq. (36)]; and dashed-dotted line, [Eq. (38)]. Here, [Eq. (37)] is the reference.

Tables

Generic image for table
Table I.

Relative kinetic energy bias due to the use of [Eq. (35)] for typical bonds of the GROMOS 43A1 force field, (Ref. 22), with energy , . Here, represents the harmonic constant and the reduced mass of the two atoms.

Generic image for table
Table II.

Average temperature calculated with the biased expression [Eq. (35)] from MD simulations at , with , and using an unbiased thermostat feedback.

Generic image for table
Table III.

Unbiased temperature and pressure from MD simulations with reference temperature and reference pressure but using the biased [Eq. (35)] for the thermostat and barostat feedback.

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/content/aip/journal/jcp/127/18/10.1063/1.2779878
2007-11-08
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/18/10.1063/1.2779878
10.1063/1.2779878
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