"Child killed: segmentation violation" error when running QM/MM minimization in QwikMD

From: Hazel, Anthony J (ahazel3_at_gatech.edu)
Date: Tue Jun 26 2018 - 17:17:28 CDT

I was trying to complete section 1.3 of the NAMD QM/MM tutorial (found here: http://www.ks.uiuc.edu/Research/qmmm/), when I encountered the following error:

child killed: segmentation violation
child killed: segmentation violation
    while executing
"::exec /Users/ahazel3/Downloads/NAMD_2.12_MacOSX-x86_64-multicore/namd2.12 +idlepoll +setcpuaffinity +p4 QMMM-Min.conf >> QMMM-Min.log"
    ("eval" body line 1)
    invoked from within
"eval ::exec [list $exec_path] [lrange $args 1 end]"
    (procedure "::ExecTool::exec" line 14)
    invoked from within
"::ExecTool::exec namd2 +idlepoll +setcpuaffinity +p4 QMMM-Min.conf >> QMMM-Min.log"
    ("eval" body line 1)
    invoked from within
"eval ::ExecTool::exec $exec_command >> $conf.log"
    (procedure "QWIKMD::Run" line 250)
    invoked from within
"QWIKMD::Run"
    invoked from within
".qwikmd.nbinput.f2.fcontrol.fcolapse.f1.run.button_Calculate invoke "
    invoked from within
".qwikmd.nbinput.f2.fcontrol.fcolapse.f1.run.button_Calculate instate {pressed !disabled} { .qwikmd.nbinput.f2.fcontrol.fcolapse.f1.run.button_Calculat..."
    (command bound to event)

I am running VMD and NAMD on macOS version 10.13.5, using VMD version 1.9.4a12 and NAMD version 2.12 (built Thu Jun 14 13:33:14 CDT 2018). I downloaded and successfully installed and tested MOPAC2016 in the /opt/mopac/ directory (found here: http://openmopac.net/Download_MOPAC_Executable_Step2.html). The given example output for the MM portion of the tutorial was used to start the QM/MM portion of the tutorial. The error occurred when running the QMMM-Min protocol listed below which was generated by QwikMD:

cutoff 12.0
pairlistdist 14.0
switching on
switchdist 10.0
PME on
PMEGridspacing 1
wrapAll on
wrapWater on
############################################################################
#cr
#cr (C) Copyright 1995-2009 The Board of Trustees of the
#cr University of Illinois
#cr All Rights Reserved
#cr
############################################################################

############################################################################
# RCS INFORMATION:
#
# $RCSfile: QMMM-Min.conf,v $
# $Author: jribeiro $ $Locker: $ $State: Exp $
# $Revision: 1.2 $ $Date: 2017/06/29 20:35:19 $
#
############################################################################
##START HERE###
##Simulation Template##
# Simulation conditions
coordinates test2_QwikMD.pdb
structure test2_QwikMD.psf

#binCoordinates qwikmdTemp.restart.coor
#binVelocities qwikmdTemp.restart.coor
extendedSystem QMMM-Min.xsc

# Simulation conditions
temperature 0

# Harmonic constraints

constraints on
consref QMMM-Min_restraints.pdb
conskfile QMMM-Min_restraints.pdb
constraintScaling 2
consexp 2
conskcol B

# Output Parameters

binaryoutput no
outputname QMMM-Min
outputenergies 1
outputtiming 1
outputpressure 1
binaryrestart yes
dcdfile QMMM-Min.dcd
dcdfreq 1
XSTFreq 1
restartfreq 1
restartname QMMM-Min.restart

# Thermostat Parameters
langevin on
langevintemp 0
langevinHydrogen on
langevindamping 50

# Barostat Parameters

usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston on
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 1

# Integrator Parameters

timestep 0.5
firstTimestep 0
fullElectFrequency 1
nonbondedfreq 1
stepspercycle 1

# Force Field Parameters

paratypecharmm on
parameters toppar_water_ions_namd.str
parameters toppar_all36_carb_glycopeptide.str
parameters par_all36_lipid.prm
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
exclude scaled1-4
1-4scaling 1.0
rigidbonds none

#Implicit Solvent Parameters

gbis off
alphaCutoff 14.0
ionConcentration 0.15

# Truns ON or OFF the QM calculations

qmForces on

#printExclusions on

# Name of a secondary PDB file where the OCCupancy
# or BETA column has the indications for QM or MM atoms.

qmParamPDB test2_QwikMD_qm-input.pdb

# Indicates qhich column has the QM/MM field.

qmColumn beta

# Number of simultaneous QM simulations per node

QMSimsPerNode 1

# Indicates qhich column has the QM-MM bond information.

qmBondColumn occ

# Indicates wether the value in the BondColumn will define the distance
# between the QM atom and the Dummy atom that will replace the MM atom

# qmBondDist on

# Indicates if the values in the bond column represent either:
# LEN: the length betwen the QM and dummy atoms.

# QMBondValueType len

# User defined Link Atom element.

#QMLinkElement "18 38 Cl"

# Indicates what will be the treatment given to QM-MM bonds in terms of
# charge distribution and dummy atom creation and placement.

QMBondScheme "CS"

# This will scale down the point charges representing the classical system
# as to replicate the switching procedure that NAMD applies to all charged
# interaction.

QMSwitching on

# This option is used to decide which kind of function will be used to scale
# down point charges sent to QM calculations.

QMSwitchingType Switch

# This will alter the point charges presented to the QM system.

QMPointChargeScheme Round

# Directory where QM calculations will be ran.

qmBaseDir [pwd]/qmmm_exec/QMMM-Min

# Indicates to NAMD that ALL forces form NAMD will be ignored and only
# the gradients from the QM software will be applied on the atoms.

qmReplaceAll OFF

# The QM code will change all QM atom's VdW types to "q"+element for VdW interactions.

QMVdWParams off

# Indicates that no Poitn Charges should be selected and applied in
# QM systems.

qmElecEmbed On

# Sets a stride for new point charge determination.

QMPCStride 1

# Indicates that one or more files will be provided with a custom selection
# of point charges.

QMCustomPCSelection off

# The file will have, in the "qmColumn", the same QM ID provided for a single QM group.

QMCustomPCFile input-CustomPC-1.0.pdb

# With Live Solvent Selection, NAMD will automatically keep track of the
# solvent molecules for all QM Groups, and will exchange classical solvent
# molecules with QM solvent molecules every "QMLSSFreq" steps.

QMLiveSolventSel off

# This indicate which residue type will be used in LSS.

QMLSSResname TIP3

# Frequency of LSS.

QMLSSFreq 50

# For LSS, this indicates how solvent molecules are selected.

QMLSSMode dist

# This will indicate which residues are to be used in the determination of the
# COM of non-solvent QM atoms.

QMLSSRef "1 RP1 9"

# The string passed to "qmConfigLine" will be copied and pasted at the very
# begining of the configuration file for the chosen QM software.

qmConfigLine PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM GEO-OK
qmConfigLine Test System

# Multiplicity of the QM region.

qmMult 1 1

# Indicates the charge of each QM region.

qmCharge 1 0.00

# Indicates which QM software should be used.

qmSoftware MOPAC

# Path to the executable

qmExecPath /opt/mopac/MOPAC2016.exe

# Charge mode expected from the QM software.

QMChargeMode mulliken

# Frequency of QM charge output.

QMOutStride 1

# Frequency of QM ONLY position output.

QMPositionOutStride 1

# Number of steps in the QM/MM simulation

# Script
minimize 100

set file [open QMMM-Min.check w+]
set done 1
if {[file exists QMMM-Min.restart.coor] != 1 || [file exists QMMM-Min.restart.vel] != 1 || [file exists QMMM-Min.restart.xsc] != 1 } {
     set done 0
}
if {$done == 1} {
    puts $file "DONE"
    flush $file
  close $file
} else {
    puts $file "One or more files failed to be written"
   flush $file
  close $file
}

Downloads - MOPAC<http://openmopac.net/Download_MOPAC_Executable_Step2.html>
openmopac.net
Downloads For current version number click here If you have a license for MOPAC2012, the MOPAC2016 license will be installed automatically.

Hybrid QM/MM NAMD - University Of Illinois<http://www.ks.uiuc.edu/Research/qmmm/>
www.ks.uiuc.edu
Hybrid QM/MM NAMD. NAMD QM/MM interface extends existing NAMD features to the quantum mechanical level, presenting features that are not yet available in any QM/MM implementation.

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