Charm++: standalone mode (not using charmrun) Charm++: scheduler running in netpoll mode. Info: NAMD 2.6b1 for MacOSX-PPC 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 Kale et al., J. Comp. Phys. 151:283-312 (1999) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 50900 for net-ppc-darwin-xlc Info: Built Fri Jul 29 18:15:41 CDT 2005 by jim on harare.ks.uiuc.edu Info: Sending usage information to NAMD developers via UDP. Sent data is: Info: 1 NAMD 2.6b1 MacOSX-PPC 1 mriv209-01.ucsf.edu adm Info: Running on 1 processors. Info: 0 kB of memory in use. Info: Configuration file is n62-NPT1.conf TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE ./N62-1/N62-2equil1.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 22000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 76.154 0 0 Info: PERIODIC CELL BASIS 2 0 74.2013 0 Info: PERIODIC CELL BASIS 3 0 0 79.083 Info: PERIODIC CELL CENTER 25.5 37 23.3 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER. 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 ./N62-1/N62-2equil1.vel Info: CENTER OF MASS MOVING? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME ./N62-1/N62-2npt1.dcd Info: DCD FREQUENCY 2500 Info: DCD FIRST STEP 24500 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME ./N62-1/N62-2npt1.xst Info: XST FREQUENCY 2500 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME ./N62-1/N62-2npt1 Info: NO RESTART FILE Info: SWITCHING ACTIVE Info: SWITCHING ON 8.5 Info: SWITCHING OFF 10 Info: PAIRLIST DISTANCE 11.5 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 5 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 19 Info: ENERGY OUTPUT STEPS 500 Info: TIMING OUTPUT STEPS 500 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 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 200 FS Info: DECAY TIME IS 500 FS Info: PISTON TEMPERATURE IS 310 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS -3.78574e-06 -3.78574e-06 -3.78574e-06 Info: CELL FLUCTUATION IS ANISOTROPIC Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-06 Info: PME EWALD COEFFICIENT 0.312341 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 80 78 82 Info: Attempting to read FFTW data from FFTW_NAMD_2.6b1_MacOSX-PPC.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.6b1_MacOSX-PPC.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 1136499457 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ./N62-1/N62-2equil1.coor Info: STRUCTURE FILE ./N62-1/N62-2wation.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_lipid.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: FIRST TIMESTEP 22000 Info: SUMMARY OF PARAMETERS: Info: 179 BONDS Info: 441 ANGLES Info: 534 DIHEDRAL Info: 49 IMPROPER Info: 89 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 44757 ATOMS Info: 30985 BONDS Info: 19979 ANGLES Info: 9033 DIHEDRALS Info: 580 IMPROPERS Info: 0 EXCLUSIONS Info: 134271 DEGREES OF FREEDOM Info: 15481 HYDROGEN GROUPS Info: TOTAL MASS = 272722 amu Info: TOTAL CHARGE = 2.86475e-06 e Info: ***************************** Info: Entering startup phase 0 with 0 kB of memory in use. Info: Entering startup phase 1 with 0 kB of memory in use. Info: Entering startup phase 2 with 0 kB of memory in use. Info: Entering startup phase 3 with 0 kB of memory in use. Info: PATCH GRID IS 4 (PERIODIC) BY 3 (PERIODIC) BY 4 (PERIODIC) Info: REMOVING COM VELOCITY -0.0458702 0.010614 -0.0126762 Info: LARGEST PATCH (18) HAS 996 ATOMS Info: Entering startup phase 4 with 0 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 0 kB of memory in use. Info: Entering startup phase 6 with 0 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 0 kB of memory in use. Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 705 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 8.47033e-22 AT 9.89634 Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.43356e-14 AT 9.94673 Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.58819e-22 AT 9.94673 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 3.38548e-16 AT 9.94673 Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 4.23516e-22 AT 9.89634 Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 1.7901e-16 AT 9.99687 Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 2.11758e-22 AT 9.94673 Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 5.86184e-16 AT 9.94673 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.75 AT 0.0441942 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.65669e-14 AT 9.94673 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 19968 AT 0.0441942 Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 6.16499e-15 AT 0.0441942 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 9.99687 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 1.84656e-14 AT 9.94673 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 1.65436e-24 AT 9.99687 Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 6.36625e-16 AT 9.94673 Info: Entering startup phase 8 with 0 kB of memory in use. Info: Finished startup with 0 kB of memory in use. TCL: Running for 122000 steps ENERGY: 22000 638.1564 1929.0560 1155.0503 115.8688 -156092.7243 13099.1009 0.0000 0.0000 27809.5629 -111345.9290 208.4502 -108734.1260 -108734.1260 208.4502 21364.0736 -121.7523 446876.3485 21364.0736 -121.7523 Info: Initial time: 1 CPUs 3.48818 s/step 20.1862 days/ns 0 kB memory Info: Initial time: 1 CPUs 3.39179 s/step 19.6284 days/ns 0 kB memory Info: Initial time: 1 CPUs 3.39418 s/step 19.6422 days/ns 0 kB memory Info: Benchmark time: 1 CPUs 3.42114 s/step 19.7982 days/ns 0 kB memory Info: Benchmark time: 1 CPUs 3.38448 s/step 19.5861 days/ns 0 kB memory TIMING: 22500 CPU: 1698.94, 3.37398/step Wall: 1720.81, 3.41601/step, 115.29 hours remaining, 0 kB of memory in use. ENERGY: 22500 5945.5968 6672.4428 1150.6994 111.9644 -168426.5018 15644.9100 0.0000 0.0000 33259.8195 -105641.0688 249.3033 -102891.1820 -104085.8790 235.0676 17955.0571 237.5447 439287.4218 1.3878 1.6716 OPENING EXTENDED SYSTEM TRAJECTORY FILE OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE AT STEP 22500 Info: Benchmark time: 1 CPUs 3.41429 s/step 19.7587 days/ns 0 kB memory TIMING: 23000 CPU: 3367.73, 3.33758/step Wall: 3396.71, 3.35179/step, 112.657 hours remaining, 0 kB of memory in use. ENERGY: 23000 10076.5233 7793.0156 1111.4222 117.7378 -169647.9877 15880.7826 0.0000 0.0000 36552.3547 -98116.1515 273.9829 -94999.0342 -95451.2920 260.0115 16024.6015 334.9432 437350.9503 -1.7170 3.3742 ERROR: Atom 918 velocity is -4.41371e+07 -2.5854e+07 1.96171e+07 (limit is 5000) ERROR: Atom 920 velocity is 45218.2 17157.3 28389.8 (limit is 5000) ERROR: Atom 2548 velocity is -5504.5 -11240.6 39.3904 (limit is 5000) ERROR: Atom 2558 velocity is 23109.2 3277.23 65229.3 (limit is 5000) ERROR: Atom 2623 velocity is 5.25913e+08 3.08173e+08 -2.34323e+08 (limit is 5000) ERROR: Atom 2627 velocity is -22920.2 -2716.54 -64738.4 (limit is 5000) ERROR: Atoms moving too fast; simulation has become unstable. FATAL ERROR: Bad global exclusion count! FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html