Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
tsoc
openmm
Commits
1898d48a
"wrappers/python/vscode:/vscode.git/clone" did not exist on "f3be4bbc9ce3e1cb822fa32a6a8b35c2b0dd8896"
Unverified
Commit
1898d48a
authored
Mar 27, 2020
by
Andy Simmonett
Browse files
Add brief blurb for NH integrator
parent
691ee619
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
28 additions
and
0 deletions
+28
-0
docs-source/usersguide/application.rst
docs-source/usersguide/application.rst
+17
-0
docs-source/usersguide/references.bib
docs-source/usersguide/references.bib
+11
-0
No files found.
docs-source/usersguide/application.rst
View file @
1898d48a
...
@@ -1059,6 +1059,23 @@ sampling, and therefore is preferred for most applications. Also note that
...
@@ -1059,6 +1059,23 @@ sampling, and therefore is preferred for most applications. Also note that
:code:`LangevinIntegrator`\ , like :code:`LangevinMiddleIntegrator`\ , is a leapfrog
:code:`LangevinIntegrator`\ , like :code:`LangevinMiddleIntegrator`\ , is a leapfrog
integrator, so the velocities are offset by half a time step from the positions.
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
Leapfrog Verlet Integrator
--------------------------
--------------------------
...
...
docs-source/usersguide/references.bib
View file @
1898d48a
...
@@ -41,6 +41,17 @@
...
@@ -41,6 +41,17 @@
doi
=
{10.1103/PhysRevLett.100.020603}
,
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
@article
{
Berendsen1987
author
=
{Berendsen,
H.
J.
C.
and
Grigera,
J.
R.
and
Straatsma,
T.
P.
}
,
author
=
{Berendsen,
H.
J.
C.
and
Grigera,
J.
R.
and
Straatsma,
T.
P.
}
,
title = {The missing term in effective pair potentials},
title = {The missing term in effective pair potentials},
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment