Wednesday, May 13, 2015

example of NVT equilibration in LAMMPS

All the simulation was carried out in the NVT ensemble.
The initial equilibration was done by heating the system from 20 K to 300 K with discrete steps of 20 K/50 ps.
After the equilibration, the systems were run at a temperature of 300 K for additional 5 ns.
Dynamics of transfer, and variance in distributions  were analyzed by heating equilibrated systems from 300 K to 400 K followed by cooling from 400 K to 300 K in discrete steps of 10 K/ 200 ps.
For accurate analyses at each temperature, the last snapshot from the heating cycles were run for more than 2 ns and data collected in the equilibrated phase as seen through block averages of
total energy.
All simulations were carried out using the LAMMPS simulation package.
The equations of motion were integrated using the velocity-Verlet algorithm using a time step
of 1 fs. For NVT ensembles, a Nosé-Hoover thermostat with a damping time of 100 fs
was used to maintain the temperature of the system.

Ref: http://www.rsc.org/suppdata/nr/c3/c3nr05671f/c3nr05671f.pdf