NPT simulation maintaining a cubic cell
Hi! I am trying to density-equilibrate water. I would like to run an NPT simulation maintaining a cubic cell. Can someone please help me set this right? I could not find it in the documentation. Also, I would like the trajectory with atoms all wrapped into the box. Currently, I have something like this set where atoms in an Atoms object with pbc="T T T". This runs with the box adjusting all lattice parameters including the angles.
# Set up an NPT ensemble with Nose-Hoover thermostat
npt = NPT(atoms, timestep=1.0*units.fs,
temperature_K=300.0,
externalstress=1.01325*units.bar,
ttime=100.0*units.fs,
pfactor=1e6*2.1*units.GPa*(units.fs**2), # = B*ptime^2 (using Bulk mod of water and ptime=1000 fs)
trajectory='npt_simulation.traj',
logfile="npt.log",
loginterval=print_interval
)
I would like to maintain a cubic cell and also wrap all atoms in the cell. I understand that these are fundamental questions but wasn't sure if there was another appropriate medium.
Thank you!