From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Sep 08 2009 - 03:13:02 CDT
Hi everyone,
it is some kind of strange to me what's going on here.
I have a membrane NPGT simulations which crashes irregularly.
The simulation was running fine for Xns (divided into 1ns runs) the Nth run
crashed with "ERROR: Constraint failure in RATTLE algorithm for atom 6091!" at
Step 16193900. Okay, no big deal so far. I run the Nth run again (from the
restart files of the previous successful run). It crashed again with "ERROR:
Constraint failure in RATTLE algorithm for atom 39616!" at Step 16337300.
Now it made it over the previous crash point and failed on another timestep
and another atom. Rerunning the Nth run a third time (again from the restart
files of the previous successful run) it successfully completed.
Now my question:
Shouldn't the Simulation crash in all three runs at the same position an atom?
Is there some random seed which causes the above behaviour? Cause I would have
expected the simulation to crash at the same point because all three runs were
started from the same restart files?
Here's my input file for the restart runs of my NPGT simulation:
(best viewed with fixed font)
-----------------------------------------------------------------------------
structure step5_assembly.xplor.psf
coordinates step6.6_equilibration.pdb
set temp 303
set outputname memb1_90
firsttimestep 16000000
# Input
set inputname memb1_90
binCoordinates run031/$inputname.restart.coor
binVelocities run031/$inputname.restart.vel
extendedSystem run031/$inputname.restart.xsc
paraTypeCharmm on
parameters par_all27_prot_lipid.prm
parameters toppar_all27_lipid_cholesterol.str
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 18
pairlistsPerCycle 2
# Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 10
# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp $temp
langevinHydrogen off
# Periodic Boundary Conditions
cellBasisVector1 90.8625 0. 0.
cellBasisVector2 0. 90.8625 0.
cellBasisVector3 0. 0. 60.
cellOrigin 0. 0. 0.
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#PMEGridSizeX 96
#PMEGridSizeY 96
#PMEGridSizeZ 60
# Constant Pressure Control (variable volume)
useGroupPressure yes
useConstantArea no
useConstantRatio no
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp $temp
SurfaceTensionTarget 1
# Output
outputName $outputname
restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
run 500000
-----------------------------------------------------------------------
Kind regards
Bjoern
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