Charm++: standalone mode (not using charmrun)
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.  
Charm++: scheduler running in netpoll mode.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> Cpu topology info:
PE to node map: 0 
Node to PE map:
Chip #0: 0 
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.7b3 for Linux-x86_64-ibverbs
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 net-linux-x86_64-ibverbs-iccstatic
Info: Built Mon Jul 5 18:57:01 CDT 2010 by jim on dakar.ks.uiuc.edu
Info: 1 NAMD  2.7b3  Linux-x86_64-ibverbs  1    s31  ssarip1
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00280213 s
Info: 41.2148 MB of memory in use based on /proc/self/stat
Info: Configuration file is NPT.conf
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   310K-init.xsc
Warning: The parameter fullElectFrequency now defaults to nonbondedFreq (1) rather than stepsPerCycle.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        500
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  70.872 0 0
Info: PERIODIC CELL BASIS 2  0 97.295 0
Info: PERIODIC CELL BASIS 3  0 0 87.775
Info: PERIODIC CELL CENTER   55.476 48.3655 23.6745
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             4000 steps
Info: FIRST LDB TIMESTEP     100
Info: LAST LDB TIMESTEP     -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
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: INITIAL TEMPERATURE    310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           const_j1_310K.dcd
Info: DCD FREQUENCY          10000
Info: DCD FIRST STEP         10000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           const_j1_310K.xst
Info: XST FREQUENCY          250
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        const_j1_310K
Info: RESTART FILENAME       restart
Info: RESTART FREQUENCY      500
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          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                 0.48
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16.48
Info: ENERGY OUTPUT STEPS    1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: PRESSURE OUTPUT STEPS  1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   310
Info: LANGEVIN DAMPING COEFFICIENT IS 5 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 310 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 0 0 0
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         72 97 89
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b3_Linux-x86_64-ibverbs.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-ibverbs.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     1336595194
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         sbox_init.pdb
Info: STRUCTURE FILE         sbox_init.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             parm99bs0_all.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     310K-init.coor
Info: SUMMARY OF PARAMETERS:
Info: 139 BONDS
Info: 338 ANGLES
Info: 192 DIHEDRAL
Info: 49 IMPROPER
Info: 0 CROSSTERM
Info: 58 VDW
Info: 0 VDW_PAIRS
Warning: VDW TYPE NAME NS MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME N2 MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME NC MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME NB MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME NA MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME ND MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME NH MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME N4 MATCHES PARAMETER TYPE NAME N*
Warning: Found 17759 H-H bonds.
Info: TIME FOR READING PSF FILE: 0.262509
Info: TIME FOR READING PDB FILE: 0.146132
Info: 
Info: Reading from binary file 310K-init.coor
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 56234 ATOMS
Info: 56383 BONDS
Info: 23304 ANGLES
Info: 8260 DIHEDRALS
Info: 497 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 54248 RIGID BONDS
Info: 114454 DEGREES OF FREEDOM
Info: 19745 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 19745 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 350359 amu
Info: TOTAL CHARGE = -0.999903 e
Info: MASS DENSITY = 0.96125 g/cm^3
Info: ATOM DENSITY = 0.0929101 atoms/A^3
Info: *****************************
Info: 
Info: Entering startup at 1.11309 s, 57.2109 MB of memory in use
Info: Startup phase 0 took 0.000149965 s, 57.2109 MB of memory in use
Info: Startup phase 1 took 0.0387039 s, 66.3047 MB of memory in use
Info: Startup phase 2 took 0.000633001 s, 66.7344 MB of memory in use
Info: PATCH GRID IS 4 (PERIODIC) BY 5 (PERIODIC) BY 5 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00790807 -0.00519464 0.00986092
Info: LARGEST PATCH (49) HAS 678 ATOMS
Info: Startup phase 3 took 0.030216 s, 76.9688 MB of memory in use
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0
Info: PME TRANS LOCATIONS: 0
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Startup phase 4 took 0.654413 s, 76.9688 MB of memory in use
Info: Startup phase 5 took 6.29425e-05 s, 76.9688 MB of memory in use
LDB: Measuring processor speeds ...Namd Central LB beign created...
 Done.
Info: Startup phase 6 took 0.00019002 s, 76.9688 MB of memory in use
Info: CREATING 3110 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: Startup phase 7 took 0.0137091 s, 80.5547 MB of memory in use
Info: Startup phase 8 took 0.000524044 s, 93.2305 MB of memory in use
Info: Finished startup at 1.85169 s, 93.2305 MB of memory in use

TCL: Running for 500 steps
PRESSURE: 0 -243.474 -162.963 97.3342 -165.67 -178.431 98.694 94.9659 98.0151 -79.9568
GPRESSURE: 0 -188.901 -152.77 121.202 -162.328 -226.125 67.033 137.802 103.251 -86.057
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0       798.3326      1700.6136      2298.3014        54.7332        -224737.2938     24047.2747         0.0000         0.0000     35349.6708        -160488.3675       310.8456   -195838.0383   -160393.9916       310.8456           -167.2870      -167.0278    605251.7436      -167.2870      -167.0278

OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 121.058
LDB: ============== END OF LOAD BALANCING =============== 121.058

Info: Initial time: 1 CPUs 1.19112 s/step 6.89308 days/ns 230.41 MB memory
LDB: ============= START OF LOAD BALANCING ============== 240.851
LDB: ============== END OF LOAD BALANCING =============== 240.851

Info: Initial time: 1 CPUs 1.19806 s/step 6.93321 days/ns 234.18 MB memory
LDB: ============= START OF LOAD BALANCING ============== 361.219
LDB: ============== END OF LOAD BALANCING =============== 361.219

Info: Initial time: 1 CPUs 1.20369 s/step 6.96581 days/ns 237.027 MB memory
LDB: ============= START OF LOAD BALANCING ============== 481.876
LDB: ============== END OF LOAD BALANCING =============== 481.876

Info: Benchmark time: 1 CPUs 1.20656 s/step 6.98241 days/ns 239.516 MB memory
Info: Benchmark time: 1 CPUs 1.20141 s/step 6.9526 days/ns 247.797 MB memory
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500
WRITING COORDINATES TO RESTART FILE AT STEP 500
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 500
FINISHED WRITING RESTART VELOCITIES
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP 500
COORDINATE DCD FILE WAS NOT CREATED
WRITING VELOCITIES TO OUTPUT FILE AT STEP 500
====================================================

WallClock: 604.190857  CPUTime: 603.908203  Memory: 252.324219 MB
Program finished.