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doc/src/Section_howto.txt
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@ -1957,19 +1957,20 @@ periodic box. By holding the two regions at different temperatures
with a "thermostatting fix"_Section_howto.html#howto_13, the energy
added to the hot region should equal the energy subtracted from the
cold region and be proportional to the heat flux moving between the
regions. See the paper by "Ikeshoji and Hafskjold"_#Ikeshoji for
details of this idea. Note that thermostatting fixes such as "fix
nvt"_fix_nh.html, "fix langevin"_fix_langevin.html, and "fix
regions. See the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji
and "Wirnsberger et al"_#howto-Wirnsberger for details of this idea.
Note that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix
langevin"_fix_langevin.html, and "fix
temp/rescale"_fix_temp_rescale.html store the cumulative energy they
add/subtract.
Alternatively, as a second method, the "fix heat"_fix_heat.html
command can used in place of thermostats on each of two regions to
add/subtract specified amounts of energy to both regions. In both
cases, the resulting temperatures of the two regions can be monitored
with the "compute temp/region" command and the temperature profile of
the intermediate region can be monitored with the "fix
ave/spatial"_fix_ave_spatial.html and "compute
Alternatively, as a second method, the "fix heat"_fix_heat.html or
"fix ehex"_fix_ehex.html commands can be used in place of thermostats
on each of two regions to add/subtract specified amounts of energy to
both regions. In both cases, the resulting temperatures of the two
regions can be monitored with the "compute temp/region" command and
the temperature profile of the intermediate region can be monitored
with the "fix ave/spatial"_fix_ave_spatial.html and "compute
ke/atom"_compute_ke_atom.html commands.
The third method is to perform a reverse non-equilibrium MD simulation
@ -2786,10 +2787,14 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).
:link(Ikeshoji)
:link(howto-Ikeshoji)
[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
:link(howto-Wirnsberger)
[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
(2015).
:link(howto-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).