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 miami.ks.uiuc.edu jcomer Info: Running on 1 processors. Info: 7604 kB of memory in use. Info: Memory usage based on mallinfo Info: Configuration file is run0.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE sample.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 1000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 33.2881 19.1965 0 Info: PERIODIC CELL BASIS 2 0 38.3931 0 Info: PERIODIC CELL BASIS 3 0 0 44.7598 Info: PERIODIC CELL CENTER 0 0 0 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 sample.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 run0.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME run0.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME run0 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME run0.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 3 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 19.5 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 100 Info: HARMONIC CONSTRAINTS ACTIVE Info: HARMONIC CONS EXP 2 Info: ELECTRIC FIELD ACTIVE Info: E-FIELD VECTOR (0, 0, 10.297) Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 295 Info: LANGEVIN DAMPING COEFFICIENTS DETERMINED FROM FILES Info: LANGEVIN DAMPING FILE: siliconRest_1.0.pdb Info: LANGEVIN DAMPING COLUMN: B 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 64 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 1163406274 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB pore_all.pdb Info: STRUCTURE FILE pore_all.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS cornell.prm Info: PARAMETERS par_silicon_ions_NEW5.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES sample.coor Info: SUMMARY OF PARAMETERS: Info: 96 BONDS Info: 229 ANGLES Info: 81 DIHEDRAL Info: 31 IMPROPER Info: 0 CROSSTERM Info: 62 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 5545 ATOMS Info: 5274 BONDS Info: 7833 ANGLES Info: 0 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 1758 CONSTRAINTS Info: 16635 DEGREES OF FREEDOM Info: 3087 HYDROGEN GROUPS Info: TOTAL MASS = 60995.4 amu Info: TOTAL CHARGE = -0.00015521 e Info: ***************************** Info: Entering startup phase 0 with 8200 kB of memory in use. Info: Entering startup phase 1 with 8200 kB of memory in use. Info: Entering startup phase 2 with 8200 kB of memory in use. Info: Entering startup phase 3 with 8200 kB of memory in use. Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 2 (PERIODIC) Info: REMOVING COM VELOCITY 0.0693648 0.00729871 -0.00942431 Info: LARGEST PATCH (1) HAS 2775 ATOMS Info: CREATING 640 COMPUTE OBJECTS Info: Entering startup phase 4 with 8200 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 9252 kB of memory in use. Info: Entering startup phase 6 with 9252 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 9252 kB of memory in use. Info: CREATING 640 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Entering startup phase 8 with 9692 kB of memory in use. Info: Finished startup with 10076 kB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 1930.2729 593.7770 0.0000 0.0000 -232615.8823 3857.7171 994.5127 -485.0913 4831.2738 -220893.4202 292.3003 -220826.7825 -220826.7825 292.3003 -716.9686 -2634.6180 57204.5172 -716.9686 -2634.6180 OPENING EXTENDED SYSTEM TRAJECTORY FILE Info: Initial time: 1 CPUs 0.181838 s/step 2.10461 days/ns 31392 kB memory TIMING: 100 CPU: 19.1191, 0.180892/step Wall: 19.4364, 0.183489/step, 0.0458723 hours remaining, 31392 kB of memory in use. ENERGY: 100 2160.1635 597.1377 0.0000 0.0000 -230966.3910 4521.2173 1135.3876 -4716.9743 6191.9887 -221077.4705 374.6258 -221012.5297 -221008.2457 347.9467 4472.6562 2794.4633 57204.5172 1648.4681 1648.5542 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 Info: Initial time: 1 CPUs 0.184707 s/step 2.13781 days/ns 32776 kB memory TIMING: 200 CPU: 37.3143, 0.181952/step Wall: 38.072, 0.186356/step, 0.0414124 hours remaining, 32776 kB of memory in use. ENERGY: 200 2191.5802 642.5915 0.0000 0.0000 -230359.8261 4819.7138 1179.9184 -6429.9242 6761.3472 -221194.5991 409.0730 -221130.3935 -221127.1538 395.1139 7253.9561 5109.4362 57204.5172 3836.3603 3824.1625 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 200 WRITING COORDINATES TO DCD FILE AT STEP 200 WRITING COORDINATES TO RESTART FILE AT STEP 200 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 200 FINISHED WRITING RESTART VELOCITIES Info: Initial time: 1 CPUs 0.183748 s/step 2.12672 days/ns 32816 kB memory TIMING: 300 CPU: 55.3786, 0.180643/step Wall: 56.6118, 0.185398/step, 0.0360496 hours remaining, 32816 kB of memory in use. ENERGY: 300 2342.8558 699.9618 0.0000 0.0000 -230293.6879 5047.7761 1219.0254 -7346.9113 7077.1833 -221253.7968 428.1816 -221189.0710 -221190.5142 420.8593 9637.6353 8056.8766 57204.5172 6554.2716 6554.7353 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 300 WRITING COORDINATES TO DCD FILE AT STEP 300 WRITING COORDINATES TO RESTART FILE AT STEP 300 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 300 FINISHED WRITING RESTART VELOCITIES Info: Benchmark time: 1 CPUs 0.186167 s/step 2.15471 days/ns 32988 kB memory TIMING: 400 CPU: 73.5448, 0.181662/step Wall: 75.3867, 0.187749/step, 0.0312916 hours remaining, 32988 kB of memory in use. ENERGY: 400 2456.3682 655.2822 0.0000 0.0000 -230231.7182 5392.7562 1278.2644 -8197.7825 7278.2798 -221368.5498 440.3483 -221304.7809 -221303.9414 437.9588 12063.9474 10237.9951 57204.5172 9929.6928 9928.4914 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 400 WRITING COORDINATES TO DCD FILE AT STEP 400 WRITING COORDINATES TO RESTART FILE AT STEP 400 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 400 FINISHED WRITING RESTART VELOCITIES Info: Benchmark time: 1 CPUs 0.193267 s/step 2.23689 days/ns 33200 kB memory TIMING: 500 CPU: 91.886, 0.183412/step Wall: 94.7137, 0.19327/step, 0.0268431 hours remaining, 33200 kB of memory in use. ENERGY: 500 2414.3896 661.9999 0.0000 0.0000 -230089.0760 5561.3658 1342.2505 -8814.2125 7479.4187 -221443.8639 452.5175 -221379.5159 -221381.2319 446.8407 13235.3196 11318.9284 57204.5172 10311.0197 10306.2618 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500 WRITING COORDINATES TO DCD FILE AT STEP 500 WRITING COORDINATES TO RESTART FILE AT STEP 500 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 500 FINISHED WRITING RESTART VELOCITIES Info: Benchmark time: 1 CPUs 0.183556 s/step 2.12449 days/ns 33200 kB memory TIMING: 600 CPU: 109.918, 0.180323/step Wall: 113.07, 0.183559/step, 0.0203955 hours remaining, 33200 kB of memory in use. ENERGY: 600 2512.1379 661.2863 0.0000 0.0000 -229632.3989 5292.8521 1289.3390 -9275.4914 7592.2054 -221560.0697 459.3413 -221497.4116 -221494.9191 453.8512 11037.4989 9263.9303 57204.5172 10109.6396 10106.2633 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 600 WRITING COORDINATES TO DCD FILE AT STEP 600 WRITING COORDINATES TO RESTART FILE AT STEP 600 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 600 FINISHED WRITING RESTART VELOCITIES TIMING: 700 CPU: 128.02, 0.181012/step Wall: 131.36, 0.182904/step, 0.015242 hours remaining, 33424 kB of memory in use. ENERGY: 700 2616.3314 693.4631 0.0000 0.0000 -230003.2571 5706.3217 1329.8826 -9651.1891 7629.4669 -221678.9806 461.5957 -221613.0466 -221621.4569 463.6114 13540.7726 12206.2698 57204.5172 10398.3542 10406.2374 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 700 WRITING COORDINATES TO DCD FILE AT STEP 700 WRITING COORDINATES TO RESTART FILE AT STEP 700 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 700 FINISHED WRITING RESTART VELOCITIES TIMING: 800 CPU: 147.221, 0.192011/step Wall: 152.09, 0.207301/step, 0.0115167 hours remaining, 33464 kB of memory in use. ENERGY: 800 2544.9611 700.4970 0.0000 0.0000 -229425.0247 5263.6366 1378.9856 -9977.1147 7725.8211 -221788.2379 467.4253 -221724.1289 -221726.3580 469.0655 12686.8884 10804.2343 57204.5172 11170.3479 11170.5738 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 800 WRITING COORDINATES TO DCD FILE AT STEP 800 WRITING COORDINATES TO RESTART FILE AT STEP 800 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 800 FINISHED WRITING RESTART VELOCITIES TIMING: 900 CPU: 165.261, 0.180403/step Wall: 171.35, 0.192594/step, 0.00534984 hours remaining, 33636 kB of memory in use. ENERGY: 900 2632.7777 681.2597 0.0000 0.0000 -229476.1077 5364.5615 1398.7833 -10401.2872 7845.8626 -221954.1501 474.6880 -221889.7995 -221891.9048 474.6059 13381.8373 11589.5170 57204.5172 11213.1057 11201.4725 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 900 WRITING COORDINATES TO DCD FILE AT STEP 900 WRITING COORDINATES TO RESTART FILE AT STEP 900 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 900 FINISHED WRITING RESTART VELOCITIES TIMING: 1000 CPU: 183.261, 0.180003/step Wall: 190.097, 0.187476/step, 0 hours remaining, 33812 kB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 1000 2643.6420 725.1251 0.0000 0.0000 -229432.5496 5416.1448 1377.3433 -10694.6966 7888.5517 -222076.4394 477.2708 -222012.8588 -222011.2759 473.8601 12985.9808 11778.8446 57204.5172 11642.7386 11649.0798 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000 WRITING COORDINATES TO DCD FILE AT STEP 1000 WRITING COORDINATES TO RESTART FILE AT STEP 1000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 1000 FINISHED WRITING RESTART VELOCITIES WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 1000 CLOSING EXTENDED SYSTEM TRAJECTORY FILE WRITING COORDINATES TO OUTPUT FILE AT STEP 1000 CLOSING COORDINATE DCD FILE WRITING VELOCITIES TO OUTPUT FILE AT STEP 1000 ========================================== WallClock: 207.171631 CPUTime: 199.808624 Memory: 33812 kB