How to use NPT ensemble to fix water density

From: Adam Fraser (
Date: Tue Aug 14 2007 - 14:28:18 CDT


While working on a small system (~1600atoms) with 2 hexadecane molecules, I
noticed water grouping during my equilibration and simulation steps. (It
looked like a bubble in my waterbox).

My professor and I concluded it was because the solvation of the system
wasn't dense enough.

As a fix I am trying to use NPT ensemble...

#.. Langevin piston pressure control ....................
LangevinPiston on
LangevinPistonTarget 1.01325 # Target pressure (bar)
LangevinPistonPeriod 200 # Oscillation period (fs)
LangevinPistonDecay 100 # Damping time scale (fs)
LangevinPistonTemp 300 # Noise temperature (K)

#.. Langevin temp ....................
langevin on # Using Langevin dynamics.
langevinTemp 300 # Temperature for Langevin calculations (K)

Using these parameters I received this error shortly into the equilibration.

   ------------- Processor 0 Exiting: Called CmiAbort ------------
   Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
   Possible solutions are to restart from a recent checkpoint,
   increase margin, or disable useFlexibleCell for liquid simulation.

I received the same error by using these parameters at the simulation step.

Since the system is so small, I thought I would try it on a system of twice
the size that I had previously worked with.. same Hdec molecules, more
water. (This system never produced any visible bubbles.) The simulation
worked without error, but the pressure values are still fluctuating
astronomically between +/-1000bar. I also noticed the total energy
fluctuates strangely back and forth from -56000 and -7500.

Can anyone help me understand what I might be doing wrong in using the NPT

Otherwise, could someone suggest a better way to achieve a greater water
density so as to avoid "bubbles" in my system?

Thanks very much.

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