RE: How to use NPT ensemble to fix water density

From: Irene Newhouse (
Date: Tue Aug 14 2007 - 14:59:59 CDT

The "periodic cell" error occurs when the updated periodic box dimensions get out of balance with your PME grid parameters. Find out the new parameters by looking at the .xsc file [that's the quickest way] & reset the PME grid parameters accordingly. Then pick up your equilibration where you left off. If you need some more specific information on any part of this, email me off-group.
Irene Newhouse

Date: Tue, 14 Aug 2007 15:28:18 -0400From: adam.n.fraser_at_gmail.comTo: namd-l_at_ks.uiuc.eduSubject: namd-l: How to use NPT ensemble to fix water densityHello,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
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