Re: FATAL ERROR: Periodic cell

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Fri Feb 01 2008 - 08:44:54 CST

Hi Jorgen,

You can restart from the point where the system crushed. The problem
happened probably because your initial system is actually too big. As
you have pressure coupling the system will shrink until reach the
desired pressure. That's my one penny.

Cheers,
Jianhui

On 2/1/08, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:
> Hi all,
>
> I am applying the periodic boundary conditions to my system using the NPT
> ensemble on a small molecule surrounded by water. I started by minimizing
> the structure, solvating the system, minimizing the solvent and then
> minimizing both(around 10.000 steps for each step). After 27000 steps of MD
> simulation of the whole system I get the following error:
>
> 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 am not using the useFlexibleCell - I have included my configuration file
> below
>
> Any advise or help appreciated - thanks in advance
>
>
>
> # Adjustable parameters
> #################################
>
> structure $psf
> coordinates $pdb
>
> outputName min_Dder
>
>
> ##################################
>
> restartfreq 500
> # 500 steps = every 1ps
> dcdfreq 2000
> xstFreq 500
>
> outputEnergies 100
> # 100 steps - every 0.2 ps
> outputTiming 1000
>
> # Shows time per step and time to completion
>
> firsttimestep 0
>
> #################################
> # Simulation parameters
> #################################
>
> # Input
> paraTypeCharmm on
>
> parameters $path
>
> temperature $temperature
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10
> # Switchdist = Cutoff - 2
>
> # Promise that atom will not move more than 2A in a cycle
> pairlistdist 14
> # Cutoff + 2
> stepspercycle 10
> # Redo pairlists every ten steps
>
> # Integrator Parameters
> timestep 0.5
> # 0.5 fs/step
> rigidBonds none
> # needed for 2fs steps
> nonbondedFreq 1
> # nonbonded forces every step
> fullElectFrequency 2
> # PME only every other step
>
> ###################################
> #
> # Temperature and Pressure control
> #
> ###################################
> ###################################
> #
> # Constant Temperature Control
> #
> ###################################
>
> if {$nve==0} {
> langevin on
> # langevin dynamics
> langevinDamping 5.
> # damping coefficient of 5/ps
> langevinTemp $temperature
> # Random noise at this level
> langevinHydrogen no
> # Do not couple bath to hydrogens
> }
> ####################################
> #
> #
> # Pressure Control
> #
> #
> ####################################
>
> if {$npt == 1} {
> langevinPiston on
> # Appling the langevinpiston for pressure control
> langevinPistonTarget 1.01325
> # One atomsheric pressure at sea level
> langevinPistonPeriod 100
> # barostat oscillation time scale for LP method
> langevinPistonDecay 50
> # barostat damping time scale for LP
> LangevinPistonTemp $temperature
> # barostat noise temperature for LP
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigid bonds
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, maybe for membrane
> }
> ######################################
> # Fixing the protein for equilibration
> # with the water
> ######################################
> if {$fix==1} {
> fixedatoms on
> fixedatomscol B
> }
>
>
>
> # Periodic Boundary conditions
>
> cellBasisVector1 $x 0. 0.
> # Vector next to image
> cellBasisVector2 0. $y 0.
> cellBasisVector3 0. 0. $z
> cellOrigin $x0 $y0 $z0
>
> wrapWater on
> wrapAll on
>
> # Particle Mesh Ewald
>
> if {$pme == 1} {
> PME yes
> PMEGridSizeX 64 ;# 3^2*2^3, close to 71.2
> PMEGridSizeY 64 ;# 2^3*3^2 , close to 71.37
> PMEGridSizeZ 64 ;# 2^7, close to 117.47
> }
>
>
> # the center of the cell
>
> minimize $min
> # lower potential energy for 1000 steps
> reinitvels $temperature
>
> run $md
>

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