From: Adam Fraser (adam.n.fraser_at_gmail.com)
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 ....................
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
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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