The initial density can be a low value. Then if you run an NPT simulation, the density would converge to a value corresponding to the thermodynamic state (N,P,T) of the system.
Arun
You can increase the box size such that the density is a low value by adjusting the xlo ylo …parameters in the data file.
Hi Arun,
Thank you for your reply. I will generate a model using a slightly lower density in Materials Studio to begin with, adjust the box limits in the data file to reduce the density further, and equilibrate it as you suggest. I understand that the sample will become more compact so that the density converges.
Regards,
Ramaswami.
Hi Arun,
Thank you for your reply. I will generate a model using a slightly lower
density in Materials Studio to begin with, adjust the box limits in the
data file to reduce the density further, and equilibrate it as you
suggest. I understand that the sample will become more compact so that the
density converges.
here is another piece of advice, that will save you a lot of time. don't
start with fix npt right away. start with a minimization, then fix nve +
langevin, then switch to fix nvt until the system has relaxed and the
pressure stabilized. only then you should switch to fix npt. if you start
with fix npt on a non-equilibrated setup, it will likely expand, and it
can take a very long time for dense systems to recover from that and reach
the density/energy equilibrium.it is always much easier to expand then to
shrink for dense systems.
axel.
Hi Axel,
Thank you for your advice. I will try the minimization, fix nve+langevin, fix nvt, fix npt procedure as you say. I see I should play with the times of the ‘fix nve + langevin’ and ‘fix nvt’ steps until the pressure has stabilized.
Regards,
Ramaswami.