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 eq2.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE eq1.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 1000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 34.1775 19.7324 0 Info: PERIODIC CELL BASIS 2 0 39.4648 0 Info: PERIODIC CELL BASIS 3 0 0 51 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 eq1.restart.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 eq2.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME eq2.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME eq2 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME eq2.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: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 295 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 200 FS Info: DECAY TIME IS 200 FS Info: PISTON TEMPERATURE IS 295 K Info: PRESSURE CONTROL IS ATOM-BASED Info: INITIAL STRAIN RATE IS 0 0 0 Info: CELL FLUCTUATION IS ANISOTROPIC 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 96 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 1163402822 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 eq1.restart.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 8488 kB of memory in use. Info: Entering startup phase 1 with 8488 kB of memory in use. Info: Entering startup phase 2 with 8488 kB of memory in use. Info: Entering startup phase 3 with 8488 kB of memory in use. Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 2 (PERIODIC) Info: REMOVING COM VELOCITY -0.0447769 0.0244147 0.114519 Info: LARGEST PATCH (0) HAS 2788 ATOMS Info: CREATING 638 COMPUTE OBJECTS Info: Entering startup phase 4 with 8636 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 10404 kB of memory in use. Info: Entering startup phase 6 with 10404 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 10404 kB of memory in use. Info: CREATING 638 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Entering startup phase 8 with 10848 kB of memory in use. Info: Finished startup with 11232 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 1456.9261 567.0778 0.0000 0.0000 -225760.3009 2754.3428 632.5386 0.0000 4853.2373 -215496.1783 293.6291 -215430.2644 -215430.2644 293.6291 -17934.8791 -19829.0353 68789.2183 -17934.8791 -19829.0353 OPENING EXTENDED SYSTEM TRAJECTORY FILE Info: Initial time: 1 CPUs 0.191565 s/step 2.21719 days/ns 33616 kB memory TIMING: 100 CPU: 20.5269, 0.187581/step Wall: 21.1551, 0.193214/step, 0.0483035 hours remaining, 33616 kB of memory in use. ENERGY: 100 1869.7165 537.9502 0.0000 0.0000 -226660.3579 1898.1762 709.4309 0.0000 5755.1918 -215889.8923 348.1989 -215824.2950 -215824.8256 330.4899 -16413.6357 -18405.2456 68158.5836 -486.5509 -497.6421 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 0.181839 s/step 2.10462 days/ns 35264 kB memory TIMING: 200 CPU: 38.0692, 0.175423/step Wall: 39.504, 0.183489/step, 0.0407754 hours remaining, 35264 kB of memory in use. ENERGY: 200 1981.9913 540.6687 0.0000 0.0000 -228661.7889 2982.3905 946.5565 0.0000 5700.6878 -216509.4942 344.9013 -216444.4246 -216447.4408 359.9585 -7364.0210 -9213.8659 67685.4688 68.6367 68.9590 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 0.181809 s/step 2.10428 days/ns 35440 kB memory TIMING: 300 CPU: 55.7135, 0.176443/step Wall: 57.8505, 0.183465/step, 0.0356737 hours remaining, 35440 kB of memory in use. ENERGY: 300 1908.6682 527.2250 0.0000 0.0000 -230184.6829 4230.1248 976.3368 0.0000 5542.9701 -216999.3581 335.3591 -216933.7691 -216942.5926 344.8384 4677.8579 2091.0258 66707.5188 -4.0772 -8.6886 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 0.181976 s/step 2.1062 days/ns 35620 kB memory TIMING: 400 CPU: 73.3129, 0.175993/step Wall: 76.2132, 0.183627/step, 0.0306045 hours remaining, 35620 kB of memory in use. ENERGY: 400 1821.8527 520.6238 0.0000 0.0000 -230627.1798 4466.5135 1059.1514 0.0000 5500.5726 -217258.4658 332.7940 -217196.4116 -217192.1395 338.6141 8522.1207 6340.2746 66190.3575 279.5642 280.2611 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 0.178029 s/step 2.06053 days/ns 35620 kB memory TIMING: 500 CPU: 90.7492, 0.174364/step Wall: 94.0164, 0.178033/step, 0.0247268 hours remaining, 35620 kB of memory in use. ENERGY: 500 1803.3382 499.6058 0.0000 0.0000 -230852.7955 4440.4966 1160.8725 0.0000 5510.2479 -217438.2346 333.3794 -217376.1348 -217372.0774 334.7066 9628.8071 7883.4910 65836.0473 532.2767 554.1942 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 0.179526 s/step 2.07785 days/ns 36108 kB memory TIMING: 600 CPU: 108.197, 0.174473/step Wall: 111.969, 0.179529/step, 0.0199476 hours remaining, 36108 kB of memory in use. ENERGY: 600 1870.0204 479.0077 0.0000 0.0000 -231367.6175 4699.7065 1144.3584 0.0000 5543.5219 -217631.0027 335.3925 -217566.8685 -217569.1512 332.0458 10678.7311 8772.8893 65348.9106 291.7519 302.4646 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: 125.602, 0.174054/step Wall: 130.279, 0.183093/step, 0.0152578 hours remaining, 36196 kB of memory in use. ENERGY: 700 1865.3030 531.7658 0.0000 0.0000 -231352.8328 4477.7664 1126.2333 0.0000 5451.1831 -217900.5813 329.8058 -217835.6397 -217841.0854 329.5147 8224.1882 6004.2459 65052.1801 232.0156 233.1540 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: 142.955, 0.173534/step Wall: 148.152, 0.178735/step, 0.00992969 hours remaining, 36196 kB of memory in use. ENERGY: 800 1926.2730 552.3324 0.0000 0.0000 -231132.3237 3984.0453 1041.7691 0.0000 5463.8190 -218164.0850 330.5703 -218102.9713 -218092.6353 324.8744 3365.1822 1993.9072 64836.9494 12.6617 22.3200 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: 160.334, 0.173784/step Wall: 165.718, 0.175655/step, 0.00487932 hours remaining, 36196 kB of memory in use. ENERGY: 900 1891.3876 564.5424 0.0000 0.0000 -230833.8476 3729.9500 965.4766 0.0000 5407.3732 -218275.1178 327.1553 -218211.6572 -218208.8555 323.5020 115.7316 -1691.3132 64738.6376 -45.9957 -40.6351 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: 177.688, 0.173544/step Wall: 183.252, 0.175346/step, 0 hours remaining, 36196 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 1938.8602 556.7655 0.0000 0.0000 -230697.0744 3530.3418 976.4058 0.0000 5203.2202 -218491.4810 314.8037 -218424.0762 -218434.9450 320.7823 -1069.2932 -2813.9928 64479.7901 -123.2810 -133.7280 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: 183.995361 CPUTime: 177.929947 Memory: 36196 kB