ABF simulation fails with "FATAL ERROR: Low global exclusion count!"

From: Maria Pikoula (maria.pikoula_at_eng.ox.ac.uk)
Date: Tue Feb 25 2014 - 11:02:24 CST

Dear all,

In my simulation of two GlcNS(6S) restrained close to each other using ABF, the simulation fails at at some point, usually after 10 or more nanoseconds. I get the following error:

FATAL ERROR: Low global exclusion count! (9601 vs 9603) System unstable or pairlistdist or cutoff too small.

Increasing the pairlistdist hasn't helped. Any ideas what may be causing this? Below I copy the configuration file and the colvars input file.

Regards,

Maria

Config. File:
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
coordinates eqlb.coor
margin 30;
numsteps 25000000
set temp 300
set outputname abf_3.7to10

firsttimestep 0

binaryoutput no
binaryrestart no

velocities eqlb.vel

paraTypeCharmm off

amber on
parmfile ../monomers_WAT.prmtop

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching off
pairlistdist 13.5

# Integrator Parameters
timestep 2
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control Using Berendsen Method (Coupling)

tCouple on
tCoupleTemp $temp
tCoupleFile temp_coupling.pdb
tCoupleCol B

wrapAll off

extendedSystem eqlb.xsc

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

# Constant Pressure Control (variable volume)
useGroupPressure yes
useFlexibleCell no
useConstantArea no

BerendsenPressure on
BerendsenPressureTarget 1.01325 ;# in bar -> 1 atm
BerendsenPressureCompressibility 4.57E-5
BerendsenPressureRelaxationTime 100
BerendsenPressureFreq 10

# Output
outputName $outputname

restartfreq 500
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

colvars on
colvarsConfig Distance_3.7to10.in

##############################################

Colvars file:

##############################################

colvarsTrajFrequency 250
colvarsRestartFrequency 20000

colvar {
  name AtomDistance
  outputAppliedForce on
  width 0.1

  lowerboundary 3.7
  upperboundary 10.0

  lowerwallconstant 10.0
  upperwallconstant 10.0

  distance {
     group1 {
        atomnumbers { 8 16 }
     }
     group2 {
        atomnumbers { 42 50 }
     }
  }
}

abf {
  colvars AtomDistance
  fullSamples 1000
  hideJacobian
}
##############################################

Maria Pikoula
Doctoral Candidate in Centre for Doctoral Training in Healthcare Innovation
Institute of Biomedical Engineering
Department of Engineering Science
University of Oxford
maria.pikoula_at_eng.ox.ac.uk

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