Re: FATAL ERROR: Must have either an initial temperature or a velocity file

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Aug 01 2019 - 08:55:49 CDT

Hi Zhihong,

Since NAMD is producing the input files, but the output files are not being generated, I would think that MOPAC cannot be executed properly.

Did you try to execute MOPAC, giving the qmmm_0.input as input file?

Please make sure that the MOPAC full path and executable are correctly defined in the NAMD configuration file (after the keyword "qmExecPath").

Best,

João

On 7/30/19, 8:55 PM, "辛志宏" <owner-namd-l_at_ks.uiuc.edu on behalf of xzhfood_at_njau.edu.cn> wrote:

    Thank you João,
    
    There are two only two files mol.in and qmmm_0.input, no output file in the fold "/home/xzhfood/4b9f/CBM_QM-MM-3/run/qmmm_exec/QMMM-Min/0".
    
    Here is the information of qmmm_0.input,
    
    PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM GEO-OK CHARGE=0
    Test System
    
    C 3.366000 1 -1.035000 1 -8.829000 1
    O 2.852000 1 -2.153000 1 -8.954000 1
    N 3.128000 1 -0.023000 1 -9.642000 1
    H 3.612000 1 0.848000 1 -9.618000 1
    C 2.306000 1 -0.277000 1 -10.825000 1
    H 2.186000 1 -1.324000 1 -11.059000 1
    C 0.855000 1 0.139000 1 -10.453000 1
    H 0.138000 1 -0.100000 1 -11.268000 1
    H 0.543000 1 -0.429000 1 -9.551000 1
    C 0.564000 1 1.566000 1 -10.199000 1
    C 0.761000 1 2.130000 1 -8.932000 1
    H 1.110000 1 1.525000 1 -8.108000 1
    C 0.703000 1 3.478000 1 -8.686000 1
    H 0.849000 1 3.887000 1 -7.698000 1
    C 0.230000 1 4.319000 1 -9.719000 1
    O 0.098000 1 5.729000 1 -9.563000 1
    H -0.318000 1 6.101000 1 -10.345000 1
    C 0.087000 1 2.419000 1 -11.205000 1
    H 0.050000 1 1.953000 1 -12.179000 1
    C 0.016000 1 3.786000 1 -10.990000 1
    H -0.385000 1 4.420000 1 -11.767000 1
    C 2.819000 1 0.412000 1 -12.113000 1
    O 3.867000 1 1.005000 1 -12.196000 1
    N 2.131000 1 0.242000 1 -13.208000 1
    H 1.334000 1 -0.350000 1 -13.303000 1
    C 2.461000 1 1.018000 1 -14.379000 1
    H 3.341000 1 1.627000 1 -14.234000 1
    C 2.634000 1 0.191000 1 -15.607000 1
    H 2.858000 1 0.836000 1 -16.483000 1
    O 1.672000 1 -0.761000 1 -15.832000 1
    H 2.104000 1 -1.576000 1 -15.565000 1
    C 3.934000 1 -0.654000 1 -15.523000 1
    H 4.150000 1 -1.296000 1 -16.404000 1
    H 4.788000 1 0.050000 1 -15.434000 1
    H 3.852000 1 -1.367000 1 -14.674000 1
    C 1.277000 1 1.920000 1 -14.596000 1
    O 0.117000 1 1.493000 1 -14.675000 1
    N 1.524000 1 3.239000 1 -14.530000 1
    H 2.436000 1 3.630000 1 -14.629000 1
    C 0.507000 1 4.324000 1 -14.700000 1
    H -0.102000 1 4.267000 1 -13.810000 1
    C 1.193000 1 5.736000 1 -14.622000 1
    H 1.892000 1 5.657000 1 -13.762000 1
    C 2.148000 1 6.096000 1 -15.830000 1
    H 1.552000 1 6.371000 1 -16.726000 1
    H 2.679000 1 7.026000 1 -15.533000 1
    H 2.816000 1 5.222000 1 -15.985000 1
    C 0.078000 1 6.735000 1 -14.324000 1
    H -0.689000 1 6.392000 1 -13.597000 1
    H 0.375000 1 7.719000 1 -13.902000 1
    H -0.563000 1 6.926000 1 -15.211000 1
    C -0.471000 1 4.283000 1 -15.875000 1
    O -1.589000 1 4.773000 1 -15.881000 1
    N -0.014000 1 3.692000 1 -16.966000 1
    H 0.854000 1 3.204000 1 -17.019000 1
    C -0.883000 1 3.439000 1 -18.127000 1
    H -0.208000 1 2.973000 1 -18.830000 1
    C -1.983000 1 2.333000 1 -17.902000 1
    H -2.983000 1 2.670000 1 -17.556000 1
    H -2.120000 1 1.933000 1 -18.930000 1
    C -1.589000 1 1.298000 1 -16.885000 1
    O -0.577000 1 0.556000 1 -17.064000 1
    O -2.401000 1 0.970000 1 -15.968000 1
    C -7.119000 1 3.595000 1 -16.684000 1
    O -6.138000 1 4.299000 1 -17.038000 1
    N -7.048000 1 2.458000 1 -15.991000 1
    H -7.779000 1 2.108000 1 -15.411000 1
    C -5.777000 1 1.723000 1 -15.743000 1
    H -4.903000 1 2.205000 1 -16.157000 1
    C -5.555000 1 1.482000 1 -14.209000 1
    H -6.426000 1 0.984000 1 -13.731000 1
    H -4.628000 1 0.905000 1 -13.999000 1
    C -5.259000 1 2.763000 1 -13.451000 1
    C -4.058000 1 3.415000 1 -13.558000 1
    H -3.314000 1 2.974000 1 -14.204000 1
    C -3.688000 1 4.430000 1 -12.643000 1
    H -2.741000 1 4.946000 1 -12.698000 1
    C -4.669000 1 4.862000 1 -11.710000 1
    O -4.411000 1 5.964000 1 -10.891000 1
    H -3.512000 1 6.243000 1 -11.079000 1
    C -6.224000 1 3.245000 1 -12.525000 1
    H -7.180000 1 2.752000 1 -12.428000 1
    C -5.948000 1 4.273000 1 -11.677000 1
    H -6.651000 1 4.709000 1 -10.982000 1
    C -5.910000 1 0.363000 1 -16.312000 1
    O -6.991000 1 -0.183000 1 -16.446000 1
    N -4.760000 1 -0.276000 1 -16.505000 1
    H -3.901000 1 0.207000 1 -16.358000 1
    C -4.698000 1 -1.666000 1 -16.846000 1
    H -5.661000 1 -2.141000 1 -16.959000 1
    C -4.014000 1 -1.949000 1 -18.229000 1
    H -3.112000 1 -1.315000 1 -18.366000 1
    O -4.961000 1 -1.848000 1 -19.293000 1
    H -5.628000 1 -2.518000 1 -19.129000 1
    C -3.572000 1 -3.399000 1 -18.356000 1
    H -2.564000 1 -3.405000 1 -17.890000 1
    H -4.128000 1 -4.258000 1 -17.922000 1
    H -3.492000 1 -3.762000 1 -19.403000 1
    C -3.909000 1 -2.258000 1 -15.690000 1
    O -2.799000 1 -1.777000 1 -15.402000 1
    N -4.487000 1 -3.254000 1 -14.921000 1
    H -5.451000 1 -3.456000 1 -15.080000 1
    C -3.901000 1 -3.886000 1 -13.760000 1
    H -3.232000 1 -3.201000 1 -13.260000 1
    C -5.004000 1 -4.254000 1 -12.732000 1
    H -5.631000 1 -5.020000 1 -13.236000 1
    H -4.407000 1 -4.679000 1 -11.896000 1
    C -5.821000 1 -3.063000 1 -12.108000 1
    H -5.103000 1 -2.285000 1 -11.771000 1
    H -6.459000 1 -2.543000 1 -12.854000 1
    C -6.510000 1 -3.595000 1 -10.909000 1
    O -5.932000 1 -3.431000 1 -9.830000 1
    N -7.626000 1 -4.223000 1 -11.014000 1
    H -8.119000 1 -4.352000 1 -10.154000 1
    H -8.172000 1 -4.218000 1 -11.852000 1
    C -0.940000 1 -6.600000 1 -15.813000 1
    O -0.093000 1 -7.463000 1 -15.833000 1
    N -0.508000 1 -5.334000 1 -15.999000 1
    H -1.116000 1 -4.551000 1 -16.099000 1
    C 0.887000 1 -4.917000 1 -16.166000 1
    H 1.537000 1 -5.780000 1 -16.178000 1
    C 1.037000 1 -4.159000 1 -17.560000 1
    H 2.141000 1 -4.038000 1 -17.594000 1
    H 0.721000 1 -4.939000 1 -18.285000 1
    C 0.295000 1 -2.844000 1 -17.592000 1
    O -0.455000 1 -2.409000 1 -16.739000 1
    N 0.524000 1 -2.038000 1 -18.630000 1
    H 0.116000 1 -1.125000 1 -18.609000 1
    H 1.177000 1 -2.272000 1 -19.349000 1
    C 1.382000 1 -4.162000 1 -15.001000 1
    O 2.192000 1 -3.275000 1 -15.040000 1
    N 0.928000 1 -4.630000 1 -13.876000 1
    H 0.325000 1 -5.424000 1 -13.878000 1
    C 1.308000 1 -4.009000 1 -12.566000 1
    H 2.133000 1 -3.332000 1 -12.727000 1
    C 0.130000 1 -3.295000 1 -11.855000 1
    H -0.680000 1 -4.023000 1 -11.635000 1
    H 0.455000 1 -2.830000 1 -10.899000 1
    C -0.537000 1 -2.266000 1 -12.708000 1
    O -0.119000 1 -1.826000 1 -13.822000 1
    O -1.657000 1 -1.874000 1 -12.201000 1
    CA -0.660000 1 -0.511000 1 -15.331000 1
    O -2.068000 1 0.226000 1 -13.382000 1
    H -1.968000 1 -0.569000 1 -12.858000 1
    H -3.003000 1 0.425000 1 -13.340000 1
    O 1.116000 1 1.006000 1 -19.167000 1
    H 0.526000 1 0.849000 1 -18.429000 1
    H 0.606000 1 1.546000 1 -19.771000 1
    H 4.023414 1 -0.847799 1 -7.979963 1
    H -1.204712 1 4.365142 1 -18.603301 1
    H -8.134899 1 3.821152 1 -17.007889 1
    H -3.313993 1 -4.766153 1 -14.022401 1
    H -2.006758 1 -6.794480 1 -15.702074 1
    H 1.737995 1 -4.755529 1 -11.898243 1
    
    
    
    There are pop up a error windows when I run "start QM/MM simulation" , I save the log file in this window and attached the picture of error infomation,
    
    
    
    ------------- Processor 0 Exiting: Called CmiAbort ------------
    Reason: FATAL ERROR: Error running command for QM forces calculation.
    
    Charm++ fatal error:
    FATAL ERROR: Error running command for QM forces calculation.
    
    ------------- Processor 0 Exiting: Called CmiAbort ------------
    Reason: FATAL ERROR: Error running command for QM forces calculation.
    
    Charm++ fatal error:
    FATAL ERROR: Error running command for QM forces calculation.
    
        while executing
    "::exec /home/xzhfood/software/NAMD_Git-2019-07-29_Linux-x86_64-multicore/namd2 +idlepoll +setcpuaffinity +p6 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 +p6 QMMM-Min.conf >> QMMM-Min.log"
        ("eval" body line 1)
        invoked from within
    "eval ::ExecTool::exec $exec_command >> $conf.log"
        (procedure "QWIKMD::Run" line 251)
        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)
    
    
    Zhihongxin
    
    
    
    
    
    
    
    
> -----Original Messages-----
> From: "Joao Ribeiro" <jribeiro_at_ks.uiuc.edu>
> Sent Time: 2019-07-30 23:27:55 (Tuesday)
> To: "辛志宏" <xzhfood_at_njau.edu.cn>
> Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: FATAL ERROR: Must have either an initial temperature or a velocity file
>
> Dear Zhihong,
>
>
>
> Inside the folder /home/xzhfood/4b9f/CBM_QM-MM-3/run/qmmm_exec/QMMM-Min/0 you should also have a MOPAC input and out files.
>
>
>
> Did you check the output file to see if there is anything wrong with the QM calculation?
>
>
>
> Best,
>
>
>
> João
>
>
>
> From: 辛志宏 <xzhfood_at_njau.edu.cn>
> Date: Tuesday, July 30, 2019 at 10:17 AM
> To: joao ribeiro <jribeiro_at_ks.uiuc.edu>
> Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Subject: Re: Re: namd-l: FATAL ERROR: Must have either an initial temperature or a velocity file
>
>
>
> Hello João,
>
> Many thanks for your kindly help and suggestion.
>
> I downloaded the data of the NAMD-QM/MM TUTORIAL provided by www.ks.uiuc.edu and loaded CBM_MM.qwikmd file in the tutorial as input file and then setup and run it step by step, and try to find the errors where it is, here is the log file, but I do not know how to correct.
>
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in Multicore mode: 6 threads
> Charm++> Using recursive bisection (scheme 3) for topology aware partitions
> Converse/Charm++ Commit ID: v6.8.2-0-g26d4bd8-namd-charm-6.8.2-build-2018-Jan-11-30463
> CharmLB> Load balancer assumes all CPUs are same.
> Charm++> cpu affinity enabled.
> Charm++> Running on 1 unique compute nodes (8-way SMP).
> Charm++> cpu topology info is gathered in 0.000 seconds.
> Info: NAMD Git-2019-07-29 for Linux-x86_64-multicore
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: for updates, documentation, and support information.
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60800 for multicore-linux64-iccstatic
> Info: Built Mon Jul 29 02:03:39 CDT 2019 by jim on belfast.ks.uiuc.edu
> Info: 1 NAMD Git-2019-07-29 Linux-x86_64-multicore 6 localhost.localdomain root
> Info: Running on 6 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 0.00410891 s
> CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue
> Info: 401.488 MB of memory in use based on /proc/self/stat
> Info: Configuration file is QMMM-Min.conf
> Info: Working in the current directory /home/xzhfood/4b9f/CBM_QM-MM-3/run
> TCL: Suspending until startup complete.
> Warning: The following variables were set in the
> Warning: configuration file but will be ignored:
> Warning: ionConcentration (GBIS)
> Warning: alphaCutoff (GBIS)
> Info: EXTENDED SYSTEM FILE QMMM-Min.xsc
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 0.5
> Info: NUMBER OF STEPS 0
> Info: STEPS PER CYCLE 1
> Info: PERIODIC CELL BASIS 1 58.8481 0 0
> Info: PERIODIC CELL BASIS 2 0 55.5702 0
> Info: PERIODIC CELL BASIS 3 0 0 69.6404
> Info: PERIODIC CELL CENTER 1.10762 0.431464 1.59686
> Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
> Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
> Info: LOAD BALANCER Centralized
> Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
> Info: LDB PERIOD 200 steps
> Info: FIRST LDB TIMESTEP 5
> Info: LAST LDB TIMESTEP -1
> Info: LDB BACKGROUND SCALING 1
> Info: HOM BACKGROUND SCALING 1
> Info: PME BACKGROUND SCALING 1
> Info: MIN ATOMS PER PATCH 40
> Info: INITIAL TEMPERATURE 0
> Info: CENTER OF MASS MOVING INITIALLY? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 ELECTROSTATICS SCALED BY 1
> Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
> Info: DCD FILENAME QMMM-Min.dcd
> Info: DCD FREQUENCY 1
> Info: DCD FIRST STEP 1
> Info: DCD FILE WILL CONTAIN UNIT CELL DATA
> Info: XST FILENAME QMMM-Min.xst
> Info: XST FREQUENCY 1
> Info: NO VELOCITY DCD OUTPUT
> Info: NO FORCE DCD OUTPUT
> Info: OUTPUT FILENAME QMMM-Min
> Info: RESTART FILENAME QMMM-Min.restart
> Info: RESTART FREQUENCY 1
> Info: BINARY RESTART FILES WILL BE USED
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 10
> Info: SWITCHING OFF 12
> Info: PAIRLIST DISTANCE 14
> Info: PAIRLIST SHRINK RATE 0.01
> Info: PAIRLIST GROW RATE 0.01
> Info: PAIRLIST TRIGGER 0.3
> Info: PAIRLISTS PER CYCLE 2
> Info: PAIRLISTS ENABLED
> Info: MARGIN 0.495
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 16.995
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> Info: TIMING OUTPUT STEPS 1
> Info: PRESSURE OUTPUT STEPS 1
> Info: HARMONIC CONSTRAINTS ACTIVE
> Info: HARMONIC CONS EXP 2
> Info: HARMONIC CONS SCALING 2
> Info: QM FORCES ACTIVE
> Info: QM PDB PARAMETER FILE: CBM_QM-MM-3_QwikMD_qm-input.pdb
> Info: QM SOFTWARE: MOPAC
> Info: QM ATOM CHARGES FROM QM SOFTWARE: MULLIKEN
> Info: QM EXECUTABLE PATH: /home/xzhfood/opt/mopac/MOPAC2016.exe
> Info: QM COLUMN: beta
> Info: QM BOND COLUMN: occ
> Info: QM WILL DETECT BONDS BETWEEN QM AND MM ATOMS.
> Info: QM-MM BOND SCHEME: Charge Shift.
> Info: QM BASE DIRECTORY: /home/xzhfood/4b9f/CBM_QM-MM-3/run/qmmm_exec/QMMM-Min
> Info: QM CONFIG LINE: PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM GEO-OK
> Info: QM CONFIG LINE: Test System
> Info: QM POINT CHARGES WILL BE SELECTED EVERY 1 STEPS.
> Info: QM Point Charge Switching: ON.
> Info: QM Point Charge SCHEME: round.
> Info: QM executions per node: 1
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 0
> Info: LANGEVIN USING BBK INTEGRATOR
> Info: LANGEVIN DAMPING COEFFICIENT IS 50 INVERSE PS
> Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
> Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
> Info: TARGET PRESSURE IS 1.01325 BAR
> Info: OSCILLATION PERIOD IS 200 FS
> Info: DECAY TIME IS 100 FS
> Info: PISTON TEMPERATURE IS 1 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 2.79525e-05 2.79525e-05 2.79525e-05
> Info: CELL FLUCTUATION IS ISOTROPIC
> Info: PARTICLE MESH EWALD (PME) ACTIVE
> Info: PME TOLERANCE 1e-06
> Info: PME EWALD COEFFICIENT 0.257952
> Info: PME INTERPOLATION ORDER 4
> Info: PME GRID DIMENSIONS 60 56 72
> Info: PME MAXIMUM GRID SPACING 1
> Info: Attempting to read FFTW data from FFTW_NAMD_Git-2019-07-29_Linux-x86_64-multicore.txt
> Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
> Info: Writing FFTW data to FFTW_NAMD_Git-2019-07-29_Linux-x86_64-multicore.txt
> Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
> Info: USING VERLET I (r-RESPA) MTS SCHEME.
> Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
> Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
> Info: RANDOM NUMBER SEED 1564498879
> Info: USE HYDROGEN BONDS? NO
> Info: COORDINATE PDB CBM_QM-MM-3_QwikMD.pdb
> Info: STRUCTURE FILE CBM_QM-MM-3_QwikMD.psf
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS toppar_water_ions_namd.str
> Info: PARAMETERS toppar_all36_carb_glycopeptide.str
> Info: PARAMETERS par_all36_lipid.prm
> Info: PARAMETERS par_all36_na.prm
> Info: PARAMETERS par_all36_prot.prm
> Info: PARAMETERS par_all36_carb.prm
> Info: PARAMETERS par_all36_cgenff.prm
> Info: PARAMETERS HL6-H_qwikmd.str
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SUMMARY OF PARAMETERS:
> Info: 919 BONDS
> Info: 2693 ANGLES
> Info: 6598 DIHEDRAL
> Info: 194 IMPROPER
> Info: 6 CROSSTERM
> Info: 350 VDW
> Info: 6 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> Info: TIME FOR READING PSF FILE: 0.546732
> Info: Reading pdb file CBM_QM-MM-3_QwikMD.pdb
> Info: TIME FOR READING PDB FILE: 0.037828
> Info:
> Info: Using the following PDB file for QM parameters: CBM_QM-MM-3_QwikMD_qm-input.pdb
> Info: Number of QM atoms (excluding Dummy atoms): 148
> Info: We found 6 QM-MM bonds.
> Info: Applying user defined multiplicity 1 to QM group ID 1
> Info: 1) Group ID: 1 ; Group size: 148 atoms ; Total PSF charge: 0
> Info: Found user defined charge 0 for QM group ID 1. Will ignore PSF charge
    
    
    

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