This directory contains 4 input scripts for carrying out NEMD
simulations of thermal gradients for a Lennard-Jones fluid and SPC/E
water using the HEX/a (fix ehex w/ hex option) and eHEX/a (fix ehex) algorithms.

All input scripts are part of the supplementary (open access) material
supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,
124104 (2015)] and allow one to reproduce the key results reported in
that paper. The full article is available for download under
https://doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081
and the supplementary material is available under
https://www.repository.cam.ac.uk/handle/1810/250539.

Each input script in.X produces two output files: 
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-> The file out.TX contains the temperature profile. Plotting coloumn
   4 against column 2 yields the results shown in Fig. 5
   (Lennard-Jones) or Fig. 6 (SPC/E).
 
-> The file out.EX contains the time evolution of the total
   energy. The difference between the initial and final values of the
   total energy in the second column corresponds to a single point in
   Fig. 2 (Lennard-Jones) or Fig. 3 (SPC/E).

The input files data.lj and data.spce contain input configurations
which were previously prepared in a non-equilibrium steady-state
(NESS).

For the Lennard-Jones system, the box contains 2000 atoms at a density
of rho*=0.8444 (reduced units). The equilibrium temperature was
T*=0.72 in reduced units. After switching on the thermostat, a
temperature gradient of about -0.02 was generated between the
reservoirs in the reference box. The SPC/E configuration contains 1024
molecules at a density of 0.95 g/cm^3. The equilibrium temperature was
about 400 K, and after switching on the thermostat a temperature
gradient of about -4.9 K/‎Å was generated.

More details can be found in the publication.


