Re: "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 - 17:48:31 CDT

There are no errors listed in the log file. The last two lines of QMMM-Min.log are:

TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 0.

Anthony Hazel
Georgia Tech
Department of Physics
Office: Howey W207
Phone: (407) 530-9608<callto:407%29%20618-4297>
email: ahazel3_at_gatech.edu

________________________________
From: Joo Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Tuesday, June 26, 2018 6:41 PM
To: namd-l_at_ks.uiuc.edu; Hazel, Anthony J
Subject: Re: namd-l: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD

Hi Anthony,

thank you for reporting the error. Could you please check the QMMM-Min.log file, created in the run folder of your simulation? Could you please share what is the error listed in the log?

Thank you

Best

Joo

On Tue, Jun 26, 2018 at 5:21 PM Hazel, Anthony J <ahazel3_at_gatech.edu<mailto:ahazel3_at_gatech.edu>> wrote:

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.htmlSCjPc&m=Xs4O7iy3K6hiP7Ke_djCcyexQ0guCZALldbMR9b8vWc&s=SUMCpwyyskdw-flZ-beZtw6at8jhNEk_OIG7r6mQxos&e=>). 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__openmopac.net_Download-5FMOPAC-5FExecutable-5FStep2.html&d=DwMFAw&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=Xs4O7iy3K6hiP7Ke_djCcyexQ0guCZALldbMR9b8vWc&s=SUMCpwyyskdw-flZ-beZtw6at8jhNEk_OIG7r6mQxos&e=>
openmopac.net<http://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<http://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.

--
...
Joo Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>
+1 (217) 3005851

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