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