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

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Jul 30 2019 - 10:27:55 CDT

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--B_3647327276_177893850--

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