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tsoc
openmm
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1898d48a
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1898d48a
authored
Mar 27, 2020
by
Andy Simmonett
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Add brief blurb for NH integrator
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691ee619
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docs-source/usersguide/application.rst
docs-source/usersguide/application.rst
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docs-source/usersguide/references.bib
docs-source/usersguide/references.bib
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docs-source/usersguide/application.rst
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1898d48a
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@@ -1059,6 +1059,23 @@ sampling, and therefore is preferred for most applications. Also note that
:code:`LangevinIntegrator`\ , like :code:`LangevinMiddleIntegrator`\ , is a leapfrog
integrator, so the velocities are offset by half a time step from the positions.
Nosé-Hoover Integrator
----------------------
The :code:`NoseHooverIntegrator` uses the same "middle" leapfrog propagation
algorithm as :code:`LangevinMiddleIntegrator`, but replaces the stochastic
temperature control with a velocity scaling algorithm that produces more
accurate transport properties :cite:`Basconi2013`. This velocity scaling
results from propagating a chain of extra variables, which slightly reduces the
computational efficiency with respect to :code:`LangevinMiddleIntegrator`. The
integrator is minimally created by specifying only the timestep::
integrator = NoseHooverIntegrator(0.004*picoseconds)
However, many optional settings may be tuned as described XXXXXXXX. Note that
for this integrator, the velocities are offset by half a time step from the
positions.
Leapfrog Verlet Integrator
--------------------------
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docs-source/usersguide/references.bib
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1898d48a
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@@ -41,6 +41,17 @@
doi
=
{10.1103/PhysRevLett.100.020603}
,
}
@article
{
Basconi2013
,
title
=
{Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations}
,
author
=
{Joseph E. Bascon and Michael R. Shirts}
,
journal
=
{Journal of Chemical Theory and Computation}
,
volume
=
{9}
,
issue
=
{7}
,
pages
=
{2887-2899}
,
year
=
{2013}
,
doi
=
{https://doi.org/10.1021/ct400109a}
}
@article
{
Berendsen1987
author
=
{Berendsen,
H.
J.
C.
and
Grigera,
J.
R.
and
Straatsma,
T.
P.
}
,
title = {The missing term in effective pair potentials},
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