Re: How to use NPT ensemble to fix water density

From: Jeffrey J. Potoff (
Date: Tue Aug 14 2007 - 15:01:35 CDT

Adam Fraser wrote:

> Hello,
> 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 ensemble?
> Otherwise, could someone suggest a better way to achieve a greater
> water density so as to avoid "bubbles" in my system?
> Thanks very much.
> -Adam

Dear Adam,

Your system is in the process of equilibrating. The simulation cell is
getting smaller and the density is going up. The "bubbles" you saw are
simply the system in the initial stages of forming a liquid phase. To
avoid this, you need to create an initial configuration that is closer
to the density of bulk water. For a system with 1600 water molecules,
this is (roughly) a cube 37x37x37 Angstrom^3. An alternative would be
to restart your simulation from the restart file generated during your
previous simulation. Eventually, you will get to the right density.
NAMD can handle volume changes, but if the change of volume is too
large, you will get the error message you posted about the periodic
becoming too small for the original patch grid.


Jeffrey J. Potoff               
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815

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