namd2_tut2_log

Charmrun> IBVERBS version of charmrun
Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
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.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> cpu affinity enabled.
Charm++> Running on 6 unique compute nodes (64-way SMP).
Charm++> cpu topology info is gathered in 0.035 seconds.
Info: NAMD 2.10 for Linux-x86_64-ibverbs
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 60601 for net-linux-x86_64-ibverbs-iccstatic
Info: Built Tue Dec 9 15:33:59 CST 2014 by jim on dakar.ks.uiuc.edu
Info: 1 NAMD  2.10  Linux-x86_64-ibverbs  128    hydra-1  amylin
Info: Running on 128 processors, 128 nodes, 6 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.119344 s
Info: 99.0977 MB of memory in use based on /proc/self/stat
Info: Configuration file is tut2.conf
Info: Working in the current directory /home/local/amylin/namd_runs/tut2_alw
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  61.567 0 0
Info: PERIODIC CELL BASIS 2  0 62.362 0
Info: PERIODIC CELL BASIS 3  0 0 66.264
Info: PERIODIC CELL CENTER   30.8211 29.1624 17.7819
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: PME BACKGROUND SCALING 1
Info: REMOVING PATCHES FROM PROCESSOR 0
Info: MIN ATOMS PER PATCH    40
Info: INITIAL TEMPERATURE    310
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           tut2-run.dcd
Info: DCD FREQUENCY          100
Info: DCD FIRST STEP         100
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           tut2-run.xst
Info: XST FREQUENCY          100
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        tut2-run
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       tut2-run.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                 0.99
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        17.49
Info: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: PRESSURE OUTPUT STEPS  100
Info: INTERACTIVE MD ACTIVE
Info: INTERACTIVE MD PORT    3000
Info: INTERACTIVE MD FREQ    1
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   310
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 310 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 0 0 0
Info:       CELL FLUCTUATION IS ANISOTROPIC
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         64 64 72
Info: PME MAXIMUM GRID SPACING    1
Info: Attempting to read FFTW data from FFTW_NAMD_2.10_Linux-x86_64-ibverbs.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.10_Linux-x86_64-ibverbs.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      2
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     1431022278
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         solvate.pdb
Info: STRUCTURE FILE         solvate.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             par_all27_prot_lipid_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS

Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
   USING VALUES  k=130  theta0=107 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 307 BONDS
Info: 769 ANGLES
Info: 1254 DIHEDRAL
Info: 81 IMPROPER
Info: 6 CROSSTERM
Info: 190 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.355796
Info: TIME FOR READING PDB FILE: 0.0494871
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 23410 ATOMS
Info: 16023 BONDS
Info: 9650 ANGLES
Info: 3293 DIHEDRALS
Info: 204 IMPROPERS
Info: 74 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 22808 RIGID BONDS
Info: 47422 DEGREES OF FREEDOM
Info: 7995 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 7995 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 141753 amu
Info: TOTAL CHARGE = 1.0021e-06 e
Info: MASS DENSITY = 0.92522 g/cm^3
Info: ATOM DENSITY = 0.0920144 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 0.597706 s, 107.484 MB of memory in use
Info: Startup phase 0 took 0.00048399 s, 107.484 MB of memory in use
Info: ADDED 28937 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.596464 s, 112.309 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00318694 s, 113.68 MB of memory in use
Info: Startup phase 3 took 0.000310898 s, 113.68 MB of memory in use
Info: Startup phase 4 took 0.000774145 s, 113.859 MB of memory in use
Info: Startup phase 5 took 0.000302792 s, 113.859 MB of memory in use
Info: PATCH GRID IS 7 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
Info: PATCH GRID IS 2-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.0423901 -0.0038836 -0.0517072
Info: LARGEST PATCH (16) HAS 408 ATOMS
Info: TORUS A SIZE 128 USING 0 1 2 3 4 5
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 6 BY 1 BY 1
Info: Placed 93.6508% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0183611 s, 118.934 MB of memory in use
Info: PME using 32 and 32 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 18 19 20 21 22 23 42 43 44 45 ...
Info: PME TRANS LOCATIONS: 6 7 8 9 10 11 30 31 32 33 ...
Info: PME USING 32 GRID NODES AND 32 TRANS NODES
Info: Startup phase 7 took 0.00722313 s, 118.934 MB of memory in use
Info: Startup phase 8 took 0.00290489 s, 119.121 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00150204 s, 119.121 MB of memory in use
Info: CREATING 2205 COMPUTE OBJECTS
Info: Interactive MD listening on port 3000.
Info: Startup phase 10 took 0.00198007 s, 119.121 MB of memory in use
Info: useSync: 1 useProxySync: 0
Info: Startup phase 11 took 0.000352859 s, 119.121 MB of memory in use
Info: Startup phase 12 took 8.60691e-05 s, 119.121 MB of memory in use
Info: Finished startup at 1.23164 s, 119.121 MB of memory in use

TCL: Minimizing for 500 steps
PRESSURE: 0 5.63084e+06 1.1698e+07 9.59469e+06 1.1698e+07 2.46061e+07 2.04317e+07 9.59469e+06 2.04317e+07 2.3612e+08
GPRESSURE: 0 5.63046e+06 1.16973e+07 9.59467e+06 1.16973e+07 2.46053e+07 2.04311e+07 9.5944e+06 2.04318e+07 2.36123e+08
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG
ENERGY:       0      7135.6061      2469.8713       263.9440        10.7318         -77937.259
0  81250017.4108         0.0000         0.0000         0.0000       81181960.3051         0.0000  81181960.3051  81181960.3051         0.0000       88785724.5439  88786370.5388    254416.7208  88785724.5439  88786370.5388

OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING 64 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 1 226460 415643 169104 415643 799037 348028 169104 348028 1.72738e+07
GPRESSURE: 1 227151 415200 169431 415093 799843 347526 168859 348544 1.72771e+07
ENERGY:       1      7136.6146      2469.4022       264.0604        10.9865         -78541.4091   5589061.6541         0.0000         0.0000         0.0000        5520401.3086         0.0000   5520401.3086   5520401.3086         0.0000        6099760.6978   6101355.8161    254416.7208   6099760.6978   6101355.8161

MINIMIZER SLOWLY MOVING 50 ATOMS WITH BAD CONTACTS DOWNHILL
The last position output (seq=1) takes 0.001 seconds, 119.121 MB of memory in use
PRESSURE: 2 18152.9 33769 243.984 33769 60600 3028.03 243.984 3028.03 2.08337e+06
GPRESSURE: 2 20003.4 33907.1 618.981 33938.6 62947.5 2555.28 200.226 3640.16 2.08574e+06
ENERGY:       2      7136.7508      2469.8106       264.0604        10.9865         -78852.9306    668785.5723         0.0000         0.0000         0.0000         599814.2500         0.0000    599814.2500    599814.2500         0.0000         720707.9365    722896.1401    254416.7208    720707.9365    722896.1401
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WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 300
LINE MINIMIZER BRACKET: DX 0.00119077 8.87972e-05 DU -60.5588 0.321072 DUDX -101481 -165.17 7420.56
WRITING COORDINATES TO DCD FILE tut2-run.dcd AT STEP 300
WRITING COORDINATES TO RESTART FILE AT STEP 300
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 300
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=300) takes 0.001 seconds, 122.793 MB of memory in use
PRESSURE: 301 -6942.71 -20.7237 -2.42685 -20.7237 -6897.49 71.912 -2.42685 71.912 -7058.36
GPRESSURE: 301 -7004.07 -17.83 20.2445 -33.008 -6971.72 67.014 -7.6035 75.3538 -7128.76
ENERGY:     301      3049.1382      2167.4278       229.0257         8.6775        -106366.1618      9530.5969         0.0000         0.0000         0.0000         -91381.2957         0.0000    -91381.2957    -91381.2957         0.0000          -6966.1857     -7034.8512    254416.7208     -6966.1857     -7034.8512

LINE MINIMIZER BRACKET: DX 0.00119077 8.87972e-06 DU -60.5588 0.00293496 DUDX -101481 -165.17 593.138
PRESSURE: 302 -6942.87 -20.8812 -2.29513 -20.8812 -6897.49 72.0257 -2.29513 72.0257 -7058.44
GPRESSURE: 302 -7004.07 -17.961 20.3121 -33.1101 -6971.57 67.1228 -7.53643 75.5033 -7128.56
ENERGY:     302      3048.9750      2167.4166       229.0209         8.6750        -106365.9788      9530.5930         0.0000         0.0000         0.0000         -91381.2983         0.0000    -91381.2983    -91381.2983         0.0000          -6966.2680     -7034.7334    254416.7208     -6966.2680     -7034.7334