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    s29  ssarip1
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00258207 s
Info: 41.9648 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    370
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   370
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 370 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     1336595204
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: 0.26744
Info: TIME FOR READING PDB FILE: 0.14583
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 1.11163 s, 57.9609 MB of memory in use
Info: Startup phase 0 took 0.000138998 s, 57.9609 MB of memory in use
Info: Startup phase 1 took 0.0378129 s, 67.0547 MB of memory in use
Info: Startup phase 2 took 0.000664949 s, 67.4844 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 0.0166783 -0.044938 -0.0273337
Info: LARGEST PATCH (49) HAS 678 ATOMS
Info: Startup phase 3 took 0.0303822 s, 77.7188 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 0.665073 s, 77.7188 MB of memory in use
Info: Startup phase 5 took 0.000108957 s, 77.7188 MB of memory in use
LDB: Measuring processor speeds ...Namd Central LB beign created...
 Done.
Info: Startup phase 6 took 0.000250101 s, 77.7188 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 0.0136359 s, 81.3047 MB of memory in use
Info: Startup phase 8 took 0.000650167 s, 93.9805 MB of memory in use
Info: Finished startup at 1.86035 s, 93.9805 MB of memory in use

TCL: Running for 500 steps
PRESSURE: 0 -6.75616 -161.107 159.025 -163.621 94.9557 129.766 156.638 129.005 236.324
GPRESSURE: 0 74.2184 -160.766 159.927 -170.132 51.8784 101.704 176.508 137.84 199.498
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        -224737.2939     24047.2747         0.0000         0.0000     42136.2224        -153701.8160       370.5229   -195838.0384   -153604.6748       370.5229            108.1745       108.5317    605251.7436       108.1745       108.5317

OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 120.522
LDB: ============== END OF LOAD BALANCING =============== 120.523

Info: Initial time: 1 CPUs 1.18562 s/step 6.86124 days/ns 230.801 MB memory
LDB: ============= START OF LOAD BALANCING ============== 239.728
LDB: ============== END OF LOAD BALANCING =============== 239.728

Info: Initial time: 1 CPUs 1.19207 s/step 6.89857 days/ns 235.66 MB memory
LDB: ============= START OF LOAD BALANCING ============== 358.835
LDB: ============== END OF LOAD BALANCING =============== 358.835

Info: Initial time: 1 CPUs 1.19103 s/step 6.89253 days/ns 238.754 MB memory
LDB: ============= START OF LOAD BALANCING ============== 477.726
LDB: ============== END OF LOAD BALANCING =============== 477.726

Info: Benchmark time: 1 CPUs 1.18882 s/step 6.87976 days/ns 241.066 MB memory
Info: Benchmark time: 1 CPUs 1.18211 s/step 6.84092 days/ns 248.84 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: 598.076233  CPUTime: 597.790100  Memory: 253.367188 MB
Program finished.