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

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Jun 27 2018 - 09:47:41 CDT

I am glad it is working and thank you for the feedback.

Best

João

On Tue, Jun 26, 2018 at 6:31 PM Hazel, Anthony J <ahazel3_at_gatech.edu> wrote:

> The beta version of QwikMD works perfectly for the minimization step.
>
>
> Anthony
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Tuesday, June 26, 2018 7:16:11 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
>
> 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--00000000000007362f056fa0b302--

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