[AMBER] A problem about periodic box dimensions happens to Tutorial 1.7

From: wangwei1669 <wangwei1669.126.com>
Date: Sat, 4 Sep 2021 16:03:23 +0800 (CST)

Hi, Amber users,

When I was following the production step of tutorial 1.7 "An Amber Lipid Force Field Tutorial: Lipid14", I encountered a error about periodic box dimensions.

I input the file 05_Prod.in into simulation:

"Lipid production 303K 125ns
  imin=0, ! Molecular dynamics
  ntx=5, ! Positions and velocities read formatted
  irest=1, ! Restart calculation
  ntc=2, ! SHAKE on for bonds with hydrogen
  ntf=2, ! No force evaluation for bonds with hydrogen
  tol=0.0000001, ! SHAKE tolerance
  nstlim=62500000, ! Number of MD steps
  ntt=3, ! Langevin thermostat
  gamma_ln=1.0, ! Collision frequency for thermostat
  temp0=303.0, ! Simulation temperature (K)
  ntpr=5000, ! Print to mdout every ntpr steps
  ntwr=500000, ! Write a restart file every ntwr steps
  ntwx=5000, ! Write to trajectory file every ntwc steps
  dt=0.002, ! Timestep (ps)
  ig=-1, ! Random seed for Langevin thermostat
  ntb=2, ! Constant pressure periodic boundary conditions
  ntp=2, ! Anisotropic pressure coupling
  cut=10.0, ! Nonbonded cutoff (Angstroms)
  ioutfm=1, ! Write binary NetCDF trajectory
  ntxo=2, ! Write binary restart file
The simulation stopped at 80 ns and I received a feedback:

"ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values.
  Your system density has likely changed by a large amount, probably from starting the simulation from a structure a long way from equilibrium.

  [Although this error can also occur if the simulation has blown up for some reason]

The GPU code does not automatically reorganize grid cells and thus you will need to restart the calculation from the previous restart file. This will generate new grid cells and allow the alculation to continue. It may be necessary to repeat this restarting multiple times if your system is a long way from an equilibrated density. Alternatively you can run with the CPU code until the density has converged and then switch back to the GPU code."
I have checked the trace file and found the water molecules are arranged desely at the initial stage but get sparsely as simulation runs. The surface of plane consisting of water is much larger than the section of lipid membrane. Does this mean my box corrupt? Could I resume the simulation at where it stopped using GPU?

Thanks for any comment.

Best regards,
Wang Wei

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Received on Sat Sep 04 2021 - 01:30:02 PDT
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