Dear lammps users,
I have simulated a protein in water solvent.
Is it correct that I specify the npt ensemble and velocity commands for these two separately? The commands I have used are presented below. I have fixed the protein in the space using these commands.
velocity protein create 300.0 4928459 mom yes rot yes dist gaussian
velocity water create 300.0 4928459 mom yes rot yes dist uniform
velocity uion create 300.0 4928459 mom yes rot yes dist uniform
It is not correct to use multiple barostats changing the same box dimension. Each box dimension may only be modified by a single fix. LAMMPS will warn about this and in most cases that will sooner or later lead to crashes or completely bogus trajectories.
Whether you initialize and thermostat groups individually or the whole system, are mostly a question of what kind of statistical mechanical entity you want to represent (or not).
To have a proper NVT or NPT ensemble, there must be only one global thermostat and barostat no other system manipulations (e.g. via fix momentum)
There is no error and the simulation runs successfully. I checked the temperature of each particle, the temperature is OK also. What do you mean by " bogus trajectories"? The problem is that when I use a single command, some particles crash. I have some separate molecules and these commands only (having separate initialization and ensemble) lead to a stable simulation but I am not sure about the results.
please provide the input and log file of such a successful simulation.