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

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Jun 26 2018 - 18:16:11 CDT

That is interesting. I was not able to reproduce that error, but here are a
few things that might lead to the error: having the CUDA version of NAMD in
the PATH, or select the CUDA version of NAMD to execute the QM-MM
simulation when prompted to indicate where namd is by VMD, or an actual
error in the conf file. The strangest part is that there was not error
message in the log file of NAMD.

Anyway, there is an updated beta version of QwikMD in the qwikmd website (
http://www.ks.uiuc.edu/Research/qwikmd/) that has some corrections to the
QM/MM interface. Please give it a try if you will.

Best

João

On Tue, Jun 26, 2018 at 6:00 PM Hazel, Anthony J <ahazel3_at_gatech.edu> wrote:

> Its looks to be running fine when I run it just in the terminal without
> using QwikMD.
>
>
> Anthony
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Tuesday, June 26, 2018 6:53:38 PM
> *To:* Hazel, Anthony J
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: "Child killed: segmentation violation" error when
> running QM/MM minimization in QwikMD
>
> Would it be possible for you to execute the following command in
> the terminal inside
> the run folder
> ​​
> ?
>
> namd2 +p4 QMMM-Min.conf >> QMMM-Min.log?
> ​ ​
> Is there more information in the log file this time?
>
> Thank you
>
> Best
>
> João
>
> On Tue, Jun 26, 2018 at 5:48 PM Hazel, Anthony J <ahazel3_at_gatech.edu>
> wrote:
>
> 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:* João 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
>
> João
>
> On Tue, Jun 26, 2018 at 5:21 PM Hazel, Anthony J <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:
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> *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
> <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=>).
> 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:
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> *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--000000000000b82ce2056f93afac--

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