Updating and improving Andersen thermostat documentation

Added mdp options for andersen thermostat, and updated to
reflect changes in 5.0, plus add a citation for one of the assertions.

Change-Id: Ia713a4f2dd39dd5224952be334d8953b6613a66e

diff --git a/manual/algorithms.tex b/manual/algorithms.tex
index f99c243adf5640013fb667669b39094c05317f3c..61a5a755994a128943878a80689d18e65b2a10c6 100644 (file)
--- a/manual/algorithms.tex
+++ b/manual/algorithms.tex
@@ -1282,27 +1282,27 @@ is written to the energy and log file.
 \subsubsection{\normindex{Andersen thermostat}}
 One simple way to maintain a thermostatted ensemble is to take an
 $NVE$ integrator and periodically re-select the velocities of the
-particles from a Maxwell-Boltzmann distribution.~\cite{Andersen80}.
+particles from a Maxwell-Boltzmann distribution.~\cite{Andersen80}
 This can either be done by randomizing all the velocities
-simultaneously (massive collision) every $\tau_T/\Dt$ steps, or by
-randomizing every particle with some small probability every timestep,
+simultaneously (massive collision) every $\tau_T/\Dt$ steps ({\tt andersen-massive}), or by
+randomizing every particle with some small probability every timestep ({\tt andersen}),
 equal to $\Dt/\tau$, where in both cases $\Dt$ is the timestep and
 $\tau_T$ is a characteristic coupling time scale.
-
 Because of the way constraints operate, all particles in the same
-constraint group must be re-randomized simultaneously.  This
-thermostat is also only possible with velocity Verlet algorithms,
+constraint group must be randomized simultaneously.  Because of
+parallelization issues, the {\tt andersen} version cannot currently (5.0) be
+used in systems with constraints. {\tt andersen-massive} can be used regardless of constraints.
+This thermostat is also currently only possible with velocity Verlet algorithms,
 because it operates directly on the velocities at each timestep.
 
-This algorithm avoids some of the ergodicity issues of other
+This algorithm completely avoids some of the ergodicity issues of other thermostatting
 algorithms, as energy cannot flow back and forth between energetically
 decoupled components of the system as in velocity scaling motions.
 However, it can slow down the kinetics of system by randomizing
 correlated motions of the system, including slowing sampling when
 $\tau_T$ is at moderate levels (less than 10 ps). This algorithm
-should therefore generally not be used when examining kinetics of the
-system, but can avoid ergodicity problems of scaling problems when
-examining thermodynamic properties.
+should therefore generally not be used when examining kinetics or
+transport properties of the system.~\cite{Basconi2013}
 
 % \ifthenelse{\equal{\gmxlite}{1}}{}{
 \subsubsection{Nos{\'e}-Hoover temperature coupling\index{Nose-Hoover temperature coupling@Nos{\'e}-Hoover temperature coupling|see{temperature coupling, Nos{\'e}-Hoover}}{\index{temperature coupling Nose-Hoover@temperature coupling Nos{\'e}-Hoover}}\index{extended ensemble}}

diff --git a/manual/monster.bib b/manual/monster.bib
index 813b053dfeaf0a84a969d087ea303be49a4f6ef2..873130aa830acf497d63d39e5b7d2f60a95a51ef 100644 (file)
--- a/manual/monster.bib
+++ b/manual/monster.bib
@@ -46,7 +46,7 @@
 @String{BTjcomp        = "J. Comp. Phys."}
 @String{BTjcp  = "J. Chem. Phys."}
 @String{BTjcsft = "J. Chem. Soc. Far. Trans."}
-@String{BTjctc  = "J. Chem. Theory Comp."}
+@String{BTjctc  = "J. Chem. Theory Comput."}
 @String{BTjmb  = "J. Mol. Biol."}
 @String{BTjmag  = "J. Magn. Reson."}
 @String{BTjmagb = "J. Magn. Reson. Ser. B"}
@@ -8603,3 +8603,13 @@ doi = {10.1063/1.463137}
   pages     = {809--817},
   year      = 2011
 }
+
+@Article{Basconi2013,
+title = {Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations},
+author = {Joseph E. Basconi and Michael R. Shirts},
+journal = BTjctc,
+volume = {9},
+number = {7},
+pages = {2887--2899},
+year  = 2013
+}

diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html
index ac74be29076cf0fca32fc0e7146b1416d86adfa8..64736bad2e53d41aaa278fc38b808188f9942c2a 100644 (file)
--- a/share/html/online/mdp_opt.html
+++ b/share/html/online/mdp_opt.html
@@ -947,6 +947,18 @@ of the temperature fluctuations at equilibrium, which is slightly
 different from a relaxation time.
 For NVT simulations the conserved energy quantity is written
 to energy and log file.</dd>
+<dt><b>andersen</b></dt>
+<dd>Temperature coupling by randomizing a fraction of the particles
+at each timestep. Reference temperature and coupling groups are selected
+as above. <b>tau-t</b> is the average time between randomization of each molecule.
+Inhibits particle dynamics somewhat, but little or no ergodicity issues. Currently
+only implemented with velocity Verlet, and not implemented with constraints.</dd>
+<dt><b>andersen-massive</b></dt>
+<dd>Temperature coupling by randomizing all particles at infrequent timesteps.
+Reference temperature and coupling groups are selected
+as above. <b>tau-t</b> is the time between randomization of all molecules.
+Inhibits particle dynamics somewhat, but little or no ergodicity issues. Currently
+only implemented with velocity Verlet.</dd>
 <dt><b>v-rescale</b></dt>
 <dd>Temperature coupling using velocity rescaling with a stochastic term
 (JCP 126, 014101).