Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.014 seconds.
Info: NAMD 2.9 for Linux-x86_64-multicore-CUDA
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 60400 for multicore-linux64-iccstatic
Info: Built Mon Apr 30 14:02:11 CDT 2012 by jim on naiad.ks.uiuc.edu
Info: 1 NAMD  2.9  Linux-x86_64-multicore-CUDA  8    epr-rokavi3  cluster
Info: Running on 8 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.041203 s
Pe 6 physical rank 6 will use CUDA device of pe 4
Pe 1 physical rank 1 will use CUDA device of pe 4
Pe 2 physical rank 2 will use CUDA device of pe 4
Pe 3 physical rank 3 will use CUDA device of pe 4
Pe 5 physical rank 5 will use CUDA device of pe 4
Pe 7 physical rank 7 will use CUDA device of pe 4
Pe 4 physical rank 4 binding to CUDA device 0 on epr-rokavi3: 'GeForce GTX 560 Ti'  Mem: 1023MB  Rev: 2.1
Pe 0 physical rank 0 will use CUDA device of pe 4
Info: 9.4375 MB of memory in use based on /proc/self/stat
Info: Configuration file is conf/03-run.conf
Info: Changed directory to conf
TCL: INPUTNAME: 'out/02-equ/00025'
TCL: OUTPUTNAME: 'out/03-run/AA/00001'
TCL: Restarting from out/02-equ/00025
TCL: running for 1020
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   out/02-equ/00025.restart.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  23.6585 0 0
Info: PERIODIC CELL BASIS 2  0 23.6585 0
Info: PERIODIC CELL BASIS 3  0 0 23.6585
Info: PERIODIC CELL CENTER   0 0 0
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
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: MIN ATOMS PER PATCH    40
Info: VELOCITY FILE          out/02-equ/00025.restart.vel
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           out/03-run/AA/00001.dcd
Info: DCD FREQUENCY          1020
Info: DCD FIRST STEP         1020
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           out/03-run/AA/00001.xst
Info: XST FREQUENCY          1020
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        out/03-run/AA/00001
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       out/03-run/AA/00001.restart
Info: RESTART FREQUENCY      1020
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
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16.5
Info: ENERGY OUTPUT STEPS    1020
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    10200
Info: COLLECTIVE VARIABLES CALCULATION REQUESTED
Info: COLLECTIVE VARIABLES CONFIGURATION   out/03-run/AA/00001.colvars
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   300
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
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         24 24 24
Info: PME MAXIMUM GRID SPACING    1
Info: Attempting to read FFTW data from FFTW_NAMD_2.9_Linux-x86_64-multicore-CUDA.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.9_Linux-x86_64-multicore-CUDA.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      1
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C2 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : WATER
Info:         ERROR TOLERANCE : 1e-05
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1343740712
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         struct/nanmad.pdb
Info: STRUCTURE FILE         struct/nanmad.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             FF/par_all22_prot.prm
Info: PARAMETERS             FF/par_all36_lipid.prm
Info: PARAMETERS             FF/par_all27_water.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     out/02-equ/00025.restart.coor
Info: SUMMARY OF PARAMETERS:
Info: 175 BONDS
Info: 455 ANGLES
Info: 621 DIHEDRAL
Info: 38 IMPROPER
Info: 6 CROSSTERM
Info: 89 VDW
Info: 4 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.00927687
Info: TIME FOR READING PDB FILE: 0.00316787
Info: 
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 1345 ATOMS
Info: 903 BONDS
Info: 477 ANGLES
Info: 41 DIHEDRALS
Info: 4 IMPROPERS
Info: 1 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 1323 RIGID BONDS
Info: 2712 DEGREES OF FREEDOM
Info: 451 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 451 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 8088.97 amu
Info: TOTAL CHARGE = 2.23517e-08 e
Info: MASS DENSITY = 1.01436 g/cm^3
Info: ATOM DENSITY = 0.101569 atoms/A^3
Info: *****************************
Info: Reading from binary file out/02-equ/00025.restart.coor
Info: 
Info: Entering startup at 0.525225 s, 18.9102 MB of memory in use
Info: Startup phase 0 took 0.000150919 s, 18.918 MB of memory in use
Info: Startup phase 1 took 0.00144506 s, 19.2578 MB of memory in use
Info: Startup phase 2 took 0.000285149 s, 19.5195 MB of memory in use
Info: Startup phase 3 took 8.4877e-05 s, 19.5195 MB of memory in use
Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC)
Info: PATCH GRID IS 2-AWAY BY 2-AWAY BY 2-AWAY
Info: Reading from binary file out/02-equ/00025.restart.vel
Info: REMOVING COM VELOCITY 0.149868 0.263683 -0.00772015
Info: LARGEST PATCH (1) HAS 180 ATOMS
Info: Startup phase 4 took 0.00106597 s, 19.9453 MB of memory in use
Info: PME using 8 and 8 processors for FFT and reciprocal sum.
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Startup phase 5 took 0.000905037 s, 20.0508 MB of memory in use
Info: Startup phase 6 took 0.00019908 s, 20.1094 MB of memory in use
Info: Startup phase 7 took 0.000564814 s, 20.3125 MB of memory in use
Info: CREATING 624 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN SLOW TABLE ENERGY: 5.0822e-21 AT 13.7818
Info: RELATIVE IMPRECISION IN SLOW TABLE ENERGY: 6.73153e-20 AT 13.7818
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 510
colvars: # colvarsRestartFrequency = 1020
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "out/03-run/AA/00001.restart.colvars.state".
colvars: The final output state file will be "out/03-run/AA/00001.colvars.state".
colvars: The trajectory file will be "out/03-run/AA/00001.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = psi
colvars:   Initializing a new "dihedral" component.
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # oneSiteSystemForce = on
colvars:     Computing system force on group 1 only
colvars:       Initializing atom group "group1".
colvars:       Atom group "group1" defined, 1 initialized: total mass = 14.007.
colvars:       Initializing atom group "group2".
colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
colvars:       Initializing atom group "group3".
colvars:       Atom group "group3" defined, 1 initialized: total mass = 12.011.
colvars:       Initializing atom group "group4".
colvars:       Atom group "group4" defined, 1 initialized: total mass = 14.007.
colvars:   All components initialized.
colvars:   # width = 5
colvars:   # lowerBoundary = -180
colvars:   # lowerWallConstant = 0
colvars:   # upperBoundary = 180
colvars:   # upperWallConstant = 0
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputSystemForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = phi
colvars:   Initializing a new "dihedral" component.
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # oneSiteSystemForce = on
colvars:     Computing system force on group 1 only
colvars:       Initializing atom group "group1".
colvars:       Atom group "group1" defined, 1 initialized: total mass = 12.011.
colvars:       Initializing atom group "group2".
colvars:       Atom group "group2" defined, 1 initialized: total mass = 14.007.
colvars:       Initializing atom group "group3".
colvars:       Atom group "group3" defined, 1 initialized: total mass = 12.011.
colvars:       Initializing atom group "group4".
colvars:       Atom group "group4" defined, 1 initialized: total mass = 12.011.
colvars:   All components initialized.
colvars:   # width = 5
colvars:   # lowerBoundary = -180
colvars:   # lowerWallConstant = 0
colvars:   # upperBoundary = 180
colvars:   # upperWallConstant = 0
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputSystemForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new "histogram" instance.
colvars:   # name = hist
colvars:   # colvars = { phi, psi }
colvars:   # outputfreq = 1020 [default]
colvars:   Histogram will be written to file out/03-run/AA/00001.hist.dat
colvars:   Finished histogram setup.
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
Pe 4 hosts 1 local and 0 remote patches for pe 4
Pe 1 hosts 1 local and 0 remote patches for pe 4
Pe 3 hosts 0 local and 1 remote patches for pe 4
Pe 7 hosts 1 local and 0 remote patches for pe 4
Pe 6 hosts 0 local and 1 remote patches for pe 4
Pe 5 hosts 0 local and 1 remote patches for pe 4
Pe 2 hosts 1 local and 0 remote patches for pe 4
Pe 0 hosts 0 local and 1 remote patches for pe 4
Info: useSync: 1 useProxySync: 0
Info: Startup phase 8 took 0.050096 s, 41.3203 MB of memory in use
Info: Startup phase 9 took 0.000221968 s, 41.3203 MB of memory in use
Info: Startup phase 10 took 0.000136137 s, 41.3477 MB of memory in use
Info: Finished startup at 0.58038 s, 41.3477 MB of memory in use

TCL: Running for 1020 steps
Pe 4 has 4 local and 4 remote patches and 500 local and 500 remote computes.
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0         1.6780        11.3812         3.3313         2.4277          -4777.9084       415.2099         0.0000         0.0000       809.2692          -3534.6111       300.3265     -4343.8803     -3532.9186       300.3265           -297.2706      -357.5035     13242.2450      -297.2706      -357.5035

OPENING EXTENDED SYSTEM TRAJECTORY FILE
Info: useSync: 1 useProxySync: 0
Info: useSync: 1 useProxySync: 0
Info: Initial time: 8 CPUs 0.00175854 s/step 0.0101767 days/ns 53.168 MB memory
Info: useSync: 1 useProxySync: 0
Info: useSync: 1 useProxySync: 0
Info: Initial time: 8 CPUs 0.00175553 s/step 0.0101593 days/ns 54.1914 MB memory
Info: useSync: 1 useProxySync: 0
Info: Initial time: 8 CPUs 0.00175202 s/step 0.010139 days/ns 54.9453 MB memory
Info: useSync: 1 useProxySync: 0
Info: Benchmark time: 8 CPUs 0.00174513 s/step 0.0100991 days/ns 54.3164 MB memory
Info: Benchmark time: 8 CPUs 0.00176274 s/step 0.010201 days/ns 54.3359 MB memory
Info: Benchmark time: 8 CPUs 0.00175798 s/step 0.0101735 days/ns 54.3789 MB memory
colvars: Writing the state file "out/03-run/AA/00001.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "out/03-run/AA/00001.colvars.traj".
colvars: Saving collective variables state to "out/03-run/AA/00001.colvars.state".
ENERGY:    1020         4.3590         9.7751         1.4935         0.3532          -4809.5761       506.5853         0.0000         0.0000       833.9733          -3453.0367       309.4944     -4287.0101     -3449.2779       305.4074           1764.1002      1696.6957     13242.2450        67.2081        66.8946

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1020
OPENING COORDINATE DCD FILE
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 1020
FINISHED WRITING RESTART VELOCITIES
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 1020
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
CLOSING COORDINATE DCD FILE
WRITING VELOCITIES TO OUTPUT FILE AT STEP 1020
====================================================

WallClock: 2.476417  CPUTime: 2.476417  Memory: 54.527344 MB
Program finished.