Stray PME grid charges detected

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Sun Apr 03 2016 - 12:49:18 CDT

Dear NAMD experts,

I am going to run a minimization and NVT simulation followed by a NPT on a
system consists of a hyperbranched polymer in water. But, I got this error:
atoms moving too fast simulation has become unstable NAMD
therefore, based on NAMD mailing list I increase the cellbasisvectorX, Y,
and Z size and decreased the time step to 0.1 but this time I got this
error:

ERROR: Stray PME grid charges detected: 2 sending to 9 for planes 32 33 34
35
ERROR: Margin is too small for 1 atoms during timestep 201933.
ERROR: Incorrect nonbonded forces and energies may be calculated!
FATAL ERROR: Low global CUDA exclusion count! (27955 vs 27959) System
unstable or pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
[0] Stack Traceback:
  [0:0] CmiAbort+0x41 [0xefde44]
  [0:1] _Z8NAMD_bugPKc+0x9e [0x64a77e]
  [0:2] _ZN10Controller16compareChecksumsEii+0x86f [0x94db2f]
  [0:3] _ZN10Controller9integrateEi+0xc8d [0x952e4d]
  [0:4] _ZN10Controller9algorithmEv+0x1b2b [0x944f6b]
  [0:5] CthStartThread+0x20 [0xef9e90]
  [0:6] [0x33af8438f0]
[0] Stack Traceback:
  [0:0] LrtsAbort+0x70 [0xefe524]
  [0:1] CmiAbortHelper+0x102 [0xefddfd]
  [0:2] CmiAbort+0x41 [0xefde44]
  [0:3] _Z8NAMD_bugPKc+0x9e [0x64a77e]
  [0:4] _ZN10Controller16compareChecksumsEii+0x86f [0x94db2f]
  [0:5] _ZN10Controller9integrateEi+0xc8d [0x952e4d]
  [0:6] _ZN10Controller9algorithmEv+0x1b2b [0x944f6b]
  [0:7] CthStartThread+0x20 [0xef9e90]
  [0:8] [0x33af8438f0]
I do not know what should I do now! Any help will be appreciated.

My configuratyion file is as follows:

# Input
paraTypeCharmm on
parameters G5-OH/par_all36_prot.prm
parameters G5-OH/par_all36_polyester.prm
temperature $temperature

# Force-Field Parameters
exclude scaled1-4 ;# These are specified by CHARMM
1-4scaling 1.0 ;# These are specified by CHARMM
cutoff 12.0 ;# may use smaller, maybe 10.0, with PME
switching on
switchdist 10.0 ;# cutoff - 2.0
pairlistdist 14.0 ;# Promise that atom won’t move more than 2A
in a cycle, cutoff + 2

# Integrator Parameters
timestep 0.1 ;# 0.1fs/step
rigidBonds water
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 2 ;# PME only every other step
stepspercycle 10 ;# redo pairlists every ten steps

# Constant Temperature Control
langevin on ;# langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 42.00 0.00 0.00 ;# vector to the next image
cellBasisVector2 0.00 62.00 0.00
cellBasisVector3 0.00 0.00 40.00
cellOrigin -12.08 -1.14 -15.83 ;# the *center* of the cell

wrapWater on ;# wrap water to central cell
wrapAll on ;# wrap other molecules too
wrapNearest off ;# use for non-rectangular cells

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
outputTiming 1000 ;# shows time per step and time to completion

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 200000
reinitvels $temperature

run 3000000 ;# 0.3 ns

Truly yours,
Farideh

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