I'm new to MD simulation and could not understand how different termstat and barostat works.
Could anybody please introduce me an illustrative references?
Thanks so much in advances.
Dear Amir,
Lets take for instance the Berendsen thermostat and barostat (Be aware that these do not produce correct distributions and are used mainly for equilibration), there are others but the idea remains.
Thermostat> What a thermostat does is to rescale the temperatures by a factor lambda every tau picoseconds. If tau_t=1ps it means that every 1ps the temperatures of all molecules will be increased or decreased by a factor lambda. See the equation on the picture.
Barostat> For the barostat, it is the pressure the one that is changed every tau_p picoseconds. This is done via rescaling the size of the simulation cell (it can be isotropic, by changing x, y and z the same amount, or anisotropic, changing every direction independently. ) For instance, if you want to decrease the pressure to reach your target, you would expand your simulation cell. The equation is on the picture.
Now, the role that tau plays is the coupling to the external bath. This is, at more constrained tau's, i.e smaller values, you would rescale velocities and cell size more frequently. This is important to equilibrate, but you don't want to mess too much by rescaling every simulation step, so for temperature a value of 1ps is usually ok and for pressure maybe 2-10ps.
I attach you a trial I did to illustrate the coupling. There are three different values of coupling: red = 0.1ps, it reaches faster the desired pressure. green=1ps takes longer and blue=10ps takes a bit longer. Be careful, although the red one seem pretty good, changing too frequently the pressure could introduce artifacts, so it is not maybe the best choice. You can perhaps equilibrate your system, and after changing to a more loose 10ps coupling or so.Or even better to a correct barostat.
Bests and enjoy your simulations.
Dear Amir,
Lets take for instance the Berendsen thermostat and barostat (Be aware that these do not produce correct distributions and are used mainly for equilibration), there are others but the idea remains.
Thermostat> What a thermostat does is to rescale the temperatures by a factor lambda every tau picoseconds. If tau_t=1ps it means that every 1ps the temperatures of all molecules will be increased or decreased by a factor lambda. See the equation on the picture.
Barostat> For the barostat, it is the pressure the one that is changed every tau_p picoseconds. This is done via rescaling the size of the simulation cell (it can be isotropic, by changing x, y and z the same amount, or anisotropic, changing every direction independently. ) For instance, if you want to decrease the pressure to reach your target, you would expand your simulation cell. The equation is on the picture.
Now, the role that tau plays is the coupling to the external bath. This is, at more constrained tau's, i.e smaller values, you would rescale velocities and cell size more frequently. This is important to equilibrate, but you don't want to mess too much by rescaling every simulation step, so for temperature a value of 1ps is usually ok and for pressure maybe 2-10ps.
I attach you a trial I did to illustrate the coupling. There are three different values of coupling: red = 0.1ps, it reaches faster the desired pressure. green=1ps takes longer and blue=10ps takes a bit longer. Be careful, although the red one seem pretty good, changing too frequently the pressure could introduce artifacts, so it is not maybe the best choice. You can perhaps equilibrate your system, and after changing to a more loose 10ps coupling or so.Or even better to a correct barostat.
Bests and enjoy your simulations.
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