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

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.