Charm++: standalone mode (not using charmrun) Info: NAMD 2.6 for Linux-amd64 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 50900 for net-linux-amd64-iccstatic Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu Info: 1 NAMD 2.6 Linux-amd64 1 tbgl-work3.physics.uiuc.edu david Info: Running on 1 processors. Info: 7476 kB of memory in use. Info: Memory usage based on mallinfo Info: Configuration file is rot-c-short.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE ../common/rot-eq-2.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 100 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 50 0 0 Info: PERIODIC CELL BASIS 2 0 50 0 Info: PERIODIC CELL BASIS 3 0 0 50 Info: PERIODIC CELL CENTER 0 0 0 Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: MAX SELF PARTITIONS 50 Info: MAX PAIR PARTITIONS 20 Info: SELF PARTITION ATOMS 125 Info: PAIR PARTITION ATOMS 200 Info: PAIR2 PARTITION ATOMS 400 Info: MIN ATOMS PER PATCH 100 Info: VELOCITY FILE ../common/rot-eq-2.vel Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME rot-c-short.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME rot-c-short.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME rot-c-short Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME rot-c-short.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 5 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 21.5 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 100 Info: TCL GLOBAL FORCES ACTIVE Info: TCL GLOBAL FORCES SCRIPT rot-c.tcl Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 288 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 48 48 48 Info: PME MAXIMUM GRID SPACING 1.5 Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-amd64.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-amd64.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4 Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS Info: RANDOM NUMBER SEED 1173743550 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ../common/ubiquitin_solvate.pdb Info: STRUCTURE FILE ../common/ubiquitin_solvate.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS ../common/par_all27_na.inp Info: PARAMETERS ../common/par_all27_prot_lipid.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES ../common/rot-eq-2.coor Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2 PREVIOUS VALUES k=130 theta0=107 k_ub=0 r_ub=0 USING VALUES k=130 theta0=107.5 k_ub=0 r_ub=0 Warning: DUPLICATE vdW ENTRY FOR DUM PREVIOUS VALUES sigma=1.7818 epsilon=0 sigma14=1.7818 epsilon14=0 USING VALUES sigma=0 epsilon=0 sigma14=0 epsilon14=0 Info: SUMMARY OF PARAMETERS: Info: 298 BONDS Info: 729 ANGLES Info: 1145 DIHEDRAL Info: 84 IMPROPER Info: 0 CROSSTERM Info: 168 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 11317 ATOMS Info: 7961 BONDS Info: 5619 ANGLES Info: 3293 DIHEDRALS Info: 204 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 33951 DEGREES OF FREEDOM Info: 3964 HYDROGEN GROUPS Info: TOTAL MASS = 69132.6 amu Info: TOTAL CHARGE = 1.0021e-06 e Info: ***************************** Info: Entering startup phase 0 with 7476 kB of memory in use. Info: Entering startup phase 1 with 7476 kB of memory in use. Info: Entering startup phase 2 with 8096 kB of memory in use. Info: Entering startup phase 3 with 8096 kB of memory in use. Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC) Info: REMOVING COM VELOCITY -0.0715685 0.0080218 -0.0901703 Info: LARGEST PATCH (7) HAS 1504 ATOMS Info: CREATING 1927 COMPUTE OBJECTS Info: Entering startup phase 4 with 10260 kB 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: Entering startup phase 5 with 10260 kB of memory in use. Info: Entering startup phase 6 with 10260 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 10260 kB of memory in use. Info: CREATING 1927 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS TCL: Linear acceleration applied: (10 0 0) Ang*ps^-2 TCL: Angular acceleration applied: (0 0 1) Rad*ps^-2 Info: Entering startup phase 8 with 14412 kB of memory in use. Info: Finished startup with 15108 kB of memory in use. TCL: Recalculating forces at 0 TCL: Center of mass = -0.192638367627 0.243249895589 -0.11600245128 TCL: atom 1: phi = -0.593067026911 TCL: Step 0: Recalculated 305 forces ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 3320.9226 2485.4973 369.2281 41.8925 -45062.6110 4213.7486 0.0000 0.0000 9511.9860 -25119.3360 281.9740 -24978.2455 -24978.2455 281.9740 452.0847 -1933.5270 125000.0000 452.0847 -1933.5270 OPENING EXTENDED SYSTEM TRAJECTORY FILE TCL: Adding atoms prior to reconfiguring forces at 9 TCL: Recalculating forces at 10 TCL: Center of mass = -0.191176087636 0.241651412656 -0.115671904146 TCL: atom 1: phi = -0.588427995046 TCL: Step 10: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 19 TCL: Recalculating forces at 20 TCL: Center of mass = -0.187265785376 0.24047635594 -0.115041034361 TCL: atom 1: phi = -0.595701933167 TCL: Step 20: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 29 TCL: Recalculating forces at 30 TCL: Center of mass = -0.185011837567 0.240568687494 -0.11493560727 TCL: atom 1: phi = -0.600225965469 TCL: Step 30: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 39 TCL: Recalculating forces at 40 TCL: Center of mass = -0.184176170047 0.240281496355 -0.114936028982 TCL: atom 1: phi = -0.605475219436 TCL: Step 40: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 49 TCL: Recalculating forces at 50 TCL: Center of mass = -0.182107057555 0.237704245451 -0.114130797981 TCL: atom 1: phi = -0.608787199807 TCL: Step 50: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 59 TCL: Recalculating forces at 60 TCL: Center of mass = -0.180757392164 0.234340508432 -0.11400975931 TCL: atom 1: phi = -0.609103858754 TCL: Step 60: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 69 TCL: Recalculating forces at 70 TCL: Center of mass = -0.178390191519 0.232978068328 -0.11382738661 TCL: atom 1: phi = -0.603998413468 TCL: Step 70: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 79 TCL: Recalculating forces at 80 TCL: Center of mass = -0.176240703105 0.233004431548 -0.113214744472 TCL: atom 1: phi = -0.599146342368 TCL: Step 80: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 89 TCL: Recalculating forces at 90 TCL: Center of mass = -0.173688611778 0.232014946792 -0.114435835169 TCL: atom 1: phi = -0.609469844636 TCL: Step 90: Recalculated 305 forces TCL: Adding atoms prior to reconfiguring forces at 99 TCL: Recalculating forces at 100 TCL: Center of mass = -0.170131956351 0.229400344101 -0.116172354322 TCL: atom 1: phi = -0.608192229573 TCL: Step 100: Recalculated 305 forces Info: Initial time: 1 CPUs 0.164623 s/step 1.90535 days/ns 52200 kB memory TIMING: 100 CPU: 16.8134, 0.161435/step Wall: 17.1621, 0.164659/step, 0 hours remaining, 52200 kB of memory in use. ENERGY: 100 3347.2241 2400.7056 376.8084 36.9826 -44895.3719 4133.5538 0.0000 0.0000 9475.2153 -25124.8821 280.8839 -24982.9912 -24982.7064 281.0238 631.6267 -1799.0313 125000.0000 -1753.4054 -1752.8517 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 100 OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE AT STEP 100 WRITING COORDINATES TO RESTART FILE AT STEP 100 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 100 FINISHED WRITING RESTART VELOCITIES WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 100 CLOSING EXTENDED SYSTEM TRAJECTORY FILE WRITING COORDINATES TO OUTPUT FILE AT STEP 100 CLOSING COORDINATE DCD FILE WRITING VELOCITIES TO OUTPUT FILE AT STEP 100 ========================================== WallClock: 37.437576 CPUTime: 36.755413 Memory: 52200 kB Program finished.