AdAA log file

Charm++>ofi> provider: psm2
Charm++>ofi> control progress: 2
Charm++>ofi> data progress: 2
Charm++>ofi> maximum inject message size: 64
Charm++>ofi> eager maximum message size: 65536 (maximum header size: 40)
Charm++>ofi> cq entries count: 8
Charm++>ofi> use inject: 1
Charm++>ofi> maximum rma size: 4294967295
Charm++>ofi> mr mode: 0x2
Charm++>ofi> use memory pool: 0
Charm++>ofi> use request cache: 0
Charm++>ofi> number of pre-allocated recvs: 8
Charm++>ofi> exchanging addresses over OFI
Charm++> Running in non-SMP mode: numPes 40
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.8.2
Warning> Randomization of virtual memory (ASLR) is turned on in the kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try running with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (40-way SMP).
Charm++> cpu topology info is gathered in 0.045 seconds.
Info: NAMD 2.12 for Linux-x86_64
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 ofi-linux-x86_64-ifort-icc
Info: Running on 40 processors, 40 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.189006 s
Info: 308.742 MB of memory in use based on /proc/self/stat
Info: Configuration file is AdAA.conf
Info: Working in the current directory /users/travis/Cameron/AdAA
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        10
Info: PERIODIC CELL BASIS 1  40.277 0 0
Info: PERIODIC CELL BASIS 2  0 34.853 0
Info: PERIODIC CELL BASIS 3  0 0 34.758
Info: PERIODIC CELL CENTER   0.294979 0.528749 0.132491
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
Info: LDB PERIOD             2000 steps
Info: FIRST LDB TIMESTEP     50
Info: LAST LDB TIMESTEP     -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH    40
Info: INITIAL TEMPERATURE    298
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           AdAA.dcd
Info: DCD FREQUENCY          2000
Info: DCD FIRST STEP         2000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        AdAA
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       AdAA.restart
Info: RESTART FREQUENCY      100
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                 2
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        18.5
Info: ENERGY OUTPUT STEPS    5000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    50000
Info: PRESSURE OUTPUT STEPS  5000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   298
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info:        TARGET PRESSURE IS 1.01325 BAR
Info:     OSCILLATION PERIOD IS 100 FS
Info:             DECAY TIME IS 50 FS
Info:     PISTON TEMPERATURE IS 298 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 0 0 0
Info:       CELL FLUCTUATION IS ISOTROPIC
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1541429880
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         AdAA_wb.pdb
Info: STRUCTURE FILE         AdAA_wb.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             /users/travis/.charmm/par_all36_prot.prm
Info: PARAMETERS             /users/travis/.charmm/par_all36_carb.prm
Info: PARAMETERS             /users/travis/.charmm/par_all36_lipid.prm
Info: PARAMETERS             /users/travis/.charmm/par_all35_ethers.prm
Info: PARAMETERS             /users/travis/.charmm/par_all36_na.prm
Info: PARAMETERS             /users/travis/.charmm/par_all36_cgenff.prm
Info: PARAMETERS             /users/travis/.charmm/toppar_water_ions_namd.str
Info: PARAMETERS             /users/travis/.charmm/toppar_all36_prot_c36_d_aminoacids.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: SUMMARY OF PARAMETERS:
Info: 991 BONDS
Info: 2959 ANGLES
Info: 7313 DIHEDRAL
Info: 202 IMPROPER
Info: 10 CROSSTERM
Info: 370 VDW
Info: 81 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CTD1 C NH1 CT1 (ATOMS 15 21 26 28)
[0] Stack Traceback:
  [0:0] CmiAbortHelper+0x57  [0x12b06d7]
  [0:1] _Z8NAMD_diePKc+0x9d  [0x66f31d]
  [0:2] _ZN10Parameters21assign_dihedral_indexEPcS0_S0_S0_P8dihedralii+0x233  [0xf5c0d3]
  [0:3] _ZN8Molecule13read_psf_fileEPcP10Parameters+0xcbb  [0xed13db]
  [0:4] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x144  [0xecf2c4]
  [0:5] _ZN9NamdState13loadStructureEPKcS1_i+0x4dd  [0xf244ed]
  [0:6] _ZN9NamdState14configListInitEP10ConfigList+0x332  [0xf26832]
  [0:7] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0xc0  [0x103d5f0]
  [0:8] TclInvokeStringCommand+0x80  [0x2b1d52560550]
  [0:9] +0x34eb2  [0x2b1d52565eb2]
  [0:10] +0x35f1e  [0x2b1d52566f1e]
  [0:11] Tcl_EvalEx+0x16  [0x2b1d52567446]
  [0:12] Tcl_FSEvalFileEx+0x202  [0x2b1d525cec12]
  [0:13] +0x47e81  [0x2b1d52578e81]
  [0:14] +0x34eb2  [0x2b1d52565eb2]
  [0:15] +0x35f1e  [0x2b1d52566f1e]
  [0:16] Tcl_EvalEx+0x16  [0x2b1d52567446]
  [0:17] Tcl_FSEvalFileEx+0x202  [0x2b1d525cec12]
  [0:18] Tcl_EvalFile+0x27  [0x2b1d525ced77]
  [0:19] _ZN9ScriptTcl4loadEPc+0x10  [0x1039ad0]
  [0:20] main+0x4ca  [0x68a04a]
  [0:21] __libc_start_main+0xf5  [0x2b1d532b6c05]
  [0:22]   [0x5cf3e9]