Charm++> Running on MPI version: 2.1 multi-thread support: 0 (max supported: -1)
Charm++> Running on 2 unique compute nodes (12-way SMP).
Charm++> Cpu topology info:
PE to node map: 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 
Node to PE map:
Chip #0: 0 1 2 3 4 5 6 7 8 9 10 11 
Chip #1: 12 13 14 15 16 17 18 19 20 21 22 23 
Charm++> cpu topology info is gathered in 0.002 seconds.
Info: NAMD 2.7b3 for Linux-x86_64-MPI
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd@ks.uiuc.edu
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 60200 for mpi-linux-x86_64-ifort-mpicxx
Info: Built Fri Aug 20 16:50:00 BST 2010 by sjr20 on planck01
Info: 1 NAMD  2.7b3  Linux-x86_64-MPI  24    west-2-2  pc104
Info: Running on 24 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00470996 s
Info: 459.324 MB of memory in use based on /proc/self/stat
Info: Configuration file is dcdanalysis2.conf
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   nachr_popcwi_ae032.restart.xsc
Warning: Setting outputEnergies to 1 due to
Warning: pairInteraction calculations
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        20000000
Info: STEPS PER CYCLE        1
Info: PERIODIC CELL BASIS 1  115.701 0 0
Info: PERIODIC CELL BASIS 2  0 118.12 0
Info: PERIODIC CELL BASIS 3  0 0 239.229
Info: PERIODIC CELL CENTER   0.0337309 0.0193593 7.8075
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 -- ASB
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: REMOVING LOAD FROM NODE 0
Info: MAX SELF PARTITIONS    20
Info: MAX PAIR PARTITIONS    8
Info: SELF PARTITION ATOMS   154
Info: SELF2 PARTITION ATOMS   154
Info: PAIR PARTITION ATOMS   318
Info: PAIR2 PARTITION ATOMS  637
Info: MIN ATOMS PER PATCH    100
Info: VELOCITY FILE          nachr_popcwi_ae032.restart.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           dcdanalysis2.dcd
Info: DCD FREQUENCY          25
Info: DCD FIRST STEP         20000025
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           dcdanalysis2.xst
Info: XST FREQUENCY          500
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        dcdanalysis2
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       dcdanalysis2.restart
Info: RESTART FREQUENCY      500
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF                 12
Info: PAIRLIST DISTANCE      13.5
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                 0.96
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16.96
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    10
Info: PRESSURE OUTPUT STEPS  500
Info: PAIR INTERACTION CALCULATIONS ACTIVE
Info: USING FLAG 1 FOR GROUP 1
Info: COMPUTING ONLY SELF INTERACTIONS FOR GROUP 1 ATOMS
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   310
Info: LANGEVIN DAMPING COEFFICIENT IS 1 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 50 FS
Info:     PISTON TEMPERATURE IS 310 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 2.08154e-05 2.08154e-05 -1.12011e-05
Info:       CELL FLUCTUATION IS ANISOTROPIC
Info:     SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE
Info: PRESSURE PROFILE CALCULATIONS ACTIVE
Info:       NUMBER OF SLABS: 1
Info:       SLAB THICKNESS: 239.229
Info:       TIMESTEPS BETWEEN DATA OUTPUT: 25
Info:       NUMBER OF ATOM TYPES: 1
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         120 120 240
Info: PME MAXIMUM GRID SPACING    1
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b3_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b3_Linux-x86_64-MPI.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: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1373642035
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         nachr_popcwi.pdb
Info: STRUCTURE FILE         nachr_popcwi.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             par_all27_prot_lipidNBFIX.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     nachr_popcwi_ae032.restart.coor
Info: FIRST TIMESTEP         20000000
Info: SUMMARY OF PARAMETERS:
Info: 185 BONDS
Info: 467 ANGLES
Info: 601 DIHEDRAL
Info: 47 IMPROPER
Info: 6 CROSSTERM
Info: 121 VDW
Info: 2 VDW_PAIRS
Info: LONG-RANGE LJ: APPLYING ANALYTICAL CORRECTIONS TO ENERGY AND PRESSURE
Info: LONG-RANGE LJ: AVERAGE A AND B COEFFICIENTS 1.61586e+07 AND 11941.7
Info: TIME FOR READING PSF FILE: 3.63906
Info: TIME FOR READING PDB FILE: 0.489826
Info: 
Info: Reading from binary file nachr_popcwi_ae032.restart.coor
Info: To read alch data from file: selexample.pdb
Info: To read alch flag data from column: 5
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 334777 ATOMS
Info: 249850 BONDS
Info: 236727 ANGLES
Info: 216001 DIHEDRALS
Info: 5637 IMPROPERS
Info: 1823 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 299616 RIGID BONDS
Info: PAIR INTERACTION GROUP 1 CONTAINS 13 ATOMS
Info: 704715 DEGREES OF FREEDOM
Info: 119648 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 119648 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 2.03547e+06 amu
Info: TOTAL CHARGE = 6.83554e-05 e
Info: MASS DENSITY = 1.03383 g/cm^3
Info: ATOM DENSITY = 0.102396 atoms/A^3
Info: *****************************
Info: 
Info: Entering startup at 4.70284 s, 589.734 MB of memory in use
Info: Startup phase 0 took 0.00488997 s, 589.734 MB of memory in use
Info: Startup phase 1 took 0.761579 s, 594.848 MB of memory in use
Info: Startup phase 2 took 0.002244 s, 594.848 MB of memory in use
Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 14 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file nachr_popcwi_ae032.restart.vel
Info: REMOVING COM VELOCITY 0.00766634 -0.0257313 -0.0168146
Info: LARGEST PATCH (215) HAS 741 ATOMS
Info: Startup phase 3 took 0.131365 s, 664.359 MB of memory in use
Info: PME using 24 and 24 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Startup phase 4 took 0.00201607 s, 664.359 MB of memory in use
Info: Startup phase 5 took 0.0330179 s, 666.645 MB of memory in use
LDB: Measuring processor speeds ...Namd Central LB beign created...
 Done.
Info: Startup phase 6 took 1.20415 s, 666.645 MB of memory in use
Info: CREATING 18849 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.26218e-29 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.34106e-29 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 5.29396e-23 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 9.34714e-23 AT 11.9974
Info: Startup phase 7 took 0.0048039 s, 666.645 MB of memory in use
Info: Startup phase 8 took 0.000195026 s, 666.645 MB of memory in use
Info: Finished startup at 6.8471 s, 666.645 MB of memory in use

dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info: Coordinate file nachr_popcwi_pi01.dcd opened for reading.
Info: Reading timestep from file.
Info: Updating unit cell from timestep.
Info: Reading from binary file nachr_popcwi_ae032.restart.vel
Info: REMOVING COM VELOCITY 0.00766634 -0.0257313 -0.0168146
TCL: Setting parameter firstTimestep to 25
TCL: Running for 0 steps
[5] Stack Traceback:
  [5:0] _ZN9Sequencer14submitHalfstepEi+0x571  [0x981591]
  [5:1] _ZN9Sequencer9integrateEv+0x548  [0x97a978]
  [5:2] _ZN9Sequencer9threadRunEPS_+0x328  [0x987968]
  [5:3] CthStartThread+0x26  [0xa043f6]
  [5:4] setJcontext+0x81  [0xa03ee1]
  [5:5] swapJcontext+0x3e  [0xa03e3e]
  [6] Charm++ Runtime: Resumed thread (CthResume+0xe0  [0xa04240])
[4] Stack Traceback:
  [4:0] _ZN9Sequencer14submitHalfstepEi+0x571  [0x981591]
  [4:1] _ZN9Sequencer9integrateEv+0x548  [0x97a978]
  [4:2] _ZN9Sequencer9threadRunEPS_+0x328  [0x987968]
  [4:3] CthStartThread+0x26  [0xa043f6]
  [4:4] setJcontext+0x81  [0xa03ee1]
  [4:5] swapJcontext+0x3e  [0xa03e3e]
  [6] Charm++ Runtime: Resumed thread (CthResume+0xe0  [0xa04240])
WARNING: there are no tuned data files appropriate for your configuration: device = shm:dapl, np = 24, ppn = 12