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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