Directory: /home/staff/sec/secdpal
Info: NAMD 2.6 for BlueGeneL
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 50912 for bluegenel
Info: Built Thu Mar 22 16:22:27 EDT 2007 by sameer77 on bgdfen1
Info: Running on 32 processors.
Info: 1038626 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is protein.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        5100
Info: STEPS PER CYCLE        10
Info: PERIODIC CELL BASIS 1  240 0 0
Info: PERIODIC CELL BASIS 2  0 248 0
Info: PERIODIC CELL BASIS 3  0 0 248
Info: PERIODIC CELL CENTER   13.87 11.8006 26.6075
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD             2000 steps
Info: FIRST LDB TIMESTEP     50
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   47
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           output.dcd
Info: DCD FREQUENCY          500
Info: DCD FIRST STEP         5600
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           output.xst
Info: XST FREQUENCY          500
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        output
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       output.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    250
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    2500
Info: PRESSURE OUTPUT STEPS  250
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         256 256 256
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_BlueGeneL.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_BlueGeneL.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     1235103283
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         ../common/promol_wb.pdb
Info: STRUCTURE FILE         ../common/promol_wb.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             ../par_all22_prot.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     ../common/promol_wb_eq.restart.coor
Info: FIRST TIMESTEP         5100
Info: SUMMARY OF PARAMETERS:
Info: 140 BONDS
Info: 356 ANGLES
Info: 459 DIHEDRAL
Info: 43 IMPROPER
Info: 6 CROSSTERM
Info: 95 VDW
Info: 0 VDW_PAIRS
Warning: Converting binary file ../common/promol_wb_eq.restart.coor
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 10138 ATOMS
Info: 7452 BONDS
Info: 6346 ANGLES
Info: 5317 DIHEDRALS
Info: 354 IMPROPERS
Info: 128 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 9111 RIGID BONDS
Info: 21303 DEGREES OF FREEDOM
Info: 3733 HYDROGEN GROUPS
Info: TOTAL MASS = 63429.4 amu
Info: TOTAL CHARGE = 6 e
Info: *****************************
Info: Entering startup phase 0 with 1038626 kB of memory in use.
Info: Entering startup phase 1 with 1038626 kB of memory in use.
Info: Entering startup phase 2 with 1038626 kB of memory in use.
Info: Entering startup phase 3 with 1038626 kB of memory in use.
Info: PATCH GRID IS 4 (PERIODIC) BY 5 (PERIODIC) BY 5 (PERIODIC)
Info: REMOVING COM VELOCITY 0.00685089 -0.0498761 0.056467
Info: LARGEST PATCH (50) HAS 4986 ATOMS
Warning: WorkDistrib: Recursive bisection fails,invoking least-load algorithm
Info: CREATING 2149 COMPUTE OBJECTS
Info: Entering startup phase 4 with 1038626 kB of memory in use.
Info: PME using 32 and 32 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: Entering startup phase 5 with 1038626 kB of memory in use.
Info: Entering startup phase 6 with 1038626 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 1038626 kB of memory in use.
Info: CREATING 2149 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 11.7447
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 6.92477e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.05879e-22 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 5.61745e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 3.38813e-21 AT 11.7447
Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 4.24069e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 3.97047e-22 AT 11.9138
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.45399e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-32 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-16 AT 11.9138
Info: Entering startup phase 8 with 1038626 kB of memory in use.
Info: Finished startup with 1038626 kB of memory in use.
TCL: Running for 500000 steps
Info: Initial time: 32 CPUs 0.733927 s/step 4.24726 days/ns 1038626 kB memory
Load Balancing: Time 1.19365e+06 Load: Average 5.36117 Max 27.778  MSGS: TOTAL 679 MAXC 28 MAXP 7  None
Info: Adjusted background load on 30 nodes.
Load Balancing: Time 1.19365e+06 Load: Average 5.49304 Max 6.58749  MSGS: TOTAL 686 MAXC 28 MAXP 11  Alg7
Warning: 2 processors are overloaded due to high background load.
Load Balancing: Time 1.19365e+06 Load: Average 5.49304 Max 6.28374  MSGS: TOTAL 725 MAXC 36 MAXP 15  Alg7
Info: Initial time: 32 CPUs 0.829524 s/step 4.80048 days/ns 1038626 kB memory
Load Balancing: Time 1.19369e+06 Load: Average 5.42557 Max 6.38358  MSGS: TOTAL 679 MAXC 28 MAXP 7  None
Warning: 2 processors are overloaded due to high background load.
Load Balancing: Time 1.19369e+06 Load: Average 5.42557 Max 6.38358  MSGS: TOTAL 725 MAXC 36 MAXP 15  Refine
PRESSURE: 5250 -3.20108 -2.00684 0.681779 -2.00684 0.724874 -0.714047 0.681779 -0.714047 0.894849
GPRESSURE: 5250 -3.53252 -1.09609 0.000948134 -1.40688 1.76201 -1.17086 0.715573 -0.939096 1.0645
PRESSAVG: 5250 0.535106 0.214679 -0.0509658 0.214679 0.55013 -0.675473 -0.0509658 -0.675473 1.95909
GPRESSAVG: 5250 0.534915 0.197369 -0.0864096 0.240221 0.550337 -0.677008 -0.0182741 -0.688137 1.94858
Info: Initial time: 32 CPUs 0.696949 s/step 4.03327 days/ns 1038626 kB memory