Simulation box of NPT

I am running a simulation to see the behavior of CNTs in solvent using the NPT command.

I thought the simulation box would shrink to fit the atoms because I am using the NPT command, but it does not.

What can I do to make the box shrink to the atomic configuration and apply PBC?


You first need to show us what you did do. Nobody can suggest changes without knowing what to change things from.

I am gonna make a guess because I’ve seen this system many times: Most likely you are placing CNTs within a very viscous polymer at ambient temperature and pressure. Given the viscosity of the system, it would take a very long time to reach the state where all the vacuum pockets were removed. A solution could be to pre-equilibrate the system using larger pressure or temperature. (1.1 KB)
DMAC240_CNT3.dat (202.0 KB)
PAN_2019.reaxFF (8.2 KB)

This is a simulation of dispersing CNTs in a DMAc solution. It was not easy to create a model with CNTs dissolved in solution from the beginning, so we put three CNTs in the center and put the solvent model on top and bottom. Afterwards, we wanted to see the behavior of CNTs in solvent through NPT equlibration. However, the size of the box could not be reduced to fit the solvent model.

My suggestion would be to use fix deform to first manually “squish” the box so that the vacuum regions are removed, and then only start an NPT simulation.

No wonder that the box didn’t shrink. You are using iso keyword in the fix npt command so the box can only change its size isotropically, try aniso instead.

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Thank you so much.
dispersion going exactly as I wanted