Hello,
I am using fix nve and fix langevin commands to run a brownian motion simulation. My question is the following: when I write fix nve, what is the energy value fixed by LAMMPS? Simulations run without need to specify the energy value at which the physical system is supposed to stay fixed according to microcanonical ensemble, so I wonder how LAMMPS assigns it automatically.
Secondly, am I right if I say that this conserved energy does not equal the hamiltonian of brownian molecules system in so far as the solvent background energy is also to be included?
Thirdly, to run my simulation I inserted a read_data where I provided LAMMPS the initial positions of my molecules while I did not provide the initial velocities and everything worked perfectly. Does in this case (when no initial velocities input is given) LAMMPS set the initial velocities by default to zero in order to perform Verlet algorithm?
Best regards,
Luca
Hello,
I am using fix nve and fix langevin commands to run a brownian motion
simulation. My question is the following: when I write fix nve, what is the
energy value fixed by LAMMPS? Simulations run without need to specify the
energy value at which the physical system is supposed to stay fixed
you are misunderstanding how an NVE ensemble comes to be. there is
nothing being "fixed" in fix nve! on the contrary, fix nve makes no
adjustment to the energy of the system at all. ...and that is how the
NVE ensemble is defined: a system in equilibrium with no exchange of
energy with its environment whatsoever. no exchange of energy implies
a constant total energy.
that doesn't mean, that there is no change in total energy when
running with fix nve in LAMMPS, specifically during equilibration.
conversely, the preservation of total energy while in equilibrium when
running with fix nve (as sole fix) is a measure of proper selection of
MD simulation parameters. for more details please refer to textbooks
on MD simulations in general and statistical thermodynamics in
particular.
according to microcanonical ensemble, so I wonder how LAMMPS assigns it
automatically.
it doesn't.
Secondly, am I right if I say that this conserved energy does not equal the
hamiltonian of brownian molecules system in so far as the solvent background
energy is also to be included?
fix langevin can tally the energy added or removed by it, and you can
add this to the total energy, which should then become the conserved
quantity (assuming equilibrium and all other settings chosen
accordingly)
Thirdly, to run my simulation I inserted a read_data where I provided LAMMPS
the initial positions of my molecules while I did not provide the initial
velocities and everything worked perfectly. Does in this case (when no
initial velocities input is given) LAMMPS set the initial velocities by
default to zero in order to perform Verlet algorithm?
unless you use the velocity command, yes:
axel.