Charm++: standalone mode (not using charmrun) 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. Charm++> Running on 1 unique compute nodes (8-way SMP). Charm++> Cpu topology info: PE to node map: 0 Node to PE map: Chip #0: 0 Charm++> cpu topology info is gathered in 0.000 seconds. Info: NAMD 2.7b3 for Linux-x86_64-ibverbs 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 60200 for net-linux-x86_64-ibverbs-iccstatic Info: Built Mon Jul 5 18:57:01 CDT 2010 by jim on dakar.ks.uiuc.edu Info: 1 NAMD 2.7b3 Linux-x86_64-ibverbs 1 s9 ssarip1 Info: Running on 1 processors. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.00272298 s Info: 41.2148 MB of memory in use based on /proc/self/stat Info: Configuration file is NPT.conf TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE 310K-init.xsc Warning: The parameter fullElectFrequency now defaults to nonbondedFreq (1) rather than stepsPerCycle. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 500 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 70.872 0 0 Info: PERIODIC CELL BASIS 2 0 97.295 0 Info: PERIODIC CELL BASIS 3 0 0 87.775 Info: PERIODIC CELL CENTER 55.476 48.3655 23.6745 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- ASB 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: MAX SELF PARTITIONS 20 Info: MAX PAIR PARTITIONS 8 Info: SELF PARTITION ATOMS 154 Info: SELF2 PARTITION ATOMS 154 Info: PAIR PARTITION ATOMS 318 Info: PAIR2 PARTITION ATOMS 637 Info: MIN ATOMS PER PATCH 100 Info: INITIAL TEMPERATURE 300 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME const_j1_310K.dcd Info: DCD FREQUENCY 10000 Info: DCD FIRST STEP 10000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME const_j1_310K.xst Info: XST FREQUENCY 250 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME const_j1_310K Info: RESTART FILENAME 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 1000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: PRESSURE OUTPUT STEPS 1000 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 300 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 300 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 72 97 89 Info: PME MAXIMUM GRID SPACING 1.5 Info: Attempting to read FFTW data from FFTW_NAMD_2.7b3_Linux-x86_64-ibverbs.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.7b3_Linux-x86_64-ibverbs.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1 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 1336463261 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB sbox_init.pdb Info: STRUCTURE FILE sbox_init.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS parm99bs0_all.prm Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES 310K-init.coor Info: SUMMARY OF PARAMETERS: Info: 139 BONDS Info: 338 ANGLES Info: 192 DIHEDRAL Info: 49 IMPROPER Info: 0 CROSSTERM Info: 58 VDW Info: 0 VDW_PAIRS Warning: VDW TYPE NAME NS MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME N2 MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME NC MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME NB MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME NA MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME ND MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME NH MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME N4 MATCHES PARAMETER TYPE NAME N* Warning: Found 17759 H-H bonds. Info: TIME FOR READING PSF FILE: 0.262444 Info: TIME FOR READING PDB FILE: 0.141849 Info: Info: Reading from binary file 310K-init.coor Info: **************************** Info: STRUCTURE SUMMARY: Info: 56234 ATOMS Info: 56383 BONDS Info: 23304 ANGLES Info: 8260 DIHEDRALS Info: 497 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 54248 RIGID BONDS Info: 114454 DEGREES OF FREEDOM Info: 19745 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 19745 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 350359 amu Info: TOTAL CHARGE = -0.999903 e Info: MASS DENSITY = 0.96125 g/cm^3 Info: ATOM DENSITY = 0.0929101 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 1.09808 s, 57.2109 MB of memory in use Info: Startup phase 0 took 0.000156879 s, 57.2109 MB of memory in use Info: Startup phase 1 took 0.038511 s, 66.3047 MB of memory in use Info: Startup phase 2 took 0.000575066 s, 66.7344 MB of memory in use Info: PATCH GRID IS 4 (PERIODIC) BY 5 (PERIODIC) BY 5 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: REMOVING COM VELOCITY 0.018501 0.0258393 0.00960341 Info: LARGEST PATCH (49) HAS 678 ATOMS Info: Startup phase 3 took 0.0301189 s, 76.9688 MB 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: Startup phase 4 took 0.664768 s, 76.9688 MB of memory in use Info: Startup phase 5 took 6.60419e-05 s, 76.9688 MB of memory in use LDB: Measuring processor speeds ...Namd Central LB beign created... Done. Info: Startup phase 6 took 0.000175953 s, 76.9688 MB of memory in use Info: CREATING 3110 COMPUTE OBJECTS Info: useSync: 1 useProxySync: 0 Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Startup phase 7 took 0.013227 s, 80.5547 MB of memory in use Info: Startup phase 8 took 0.00051403 s, 93.2305 MB of memory in use Info: Finished startup at 1.84619 s, 93.2305 MB of memory in use TCL: Running for 500 steps PRESSURE: 0 -289.094 -133.432 132.346 -135.959 -255.903 115.354 130.013 114.597 -87.6114 GPRESSURE: 0 -228.878 -138.165 143.402 -147.543 -289.417 80.616 160.037 116.756 -113.23 ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 798.3326 1700.6136 2298.3014 54.7332 -224737.2939 24047.2747 0.0000 0.0000 34155.8376 -161682.2007 300.3477 -195838.0384 -161588.3320 300.3477 -210.8694 -210.5085 605251.7436 -210.8694 -210.5085 OPENING EXTENDED SYSTEM TRAJECTORY FILE