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.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 90 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.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 1163412205 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB pore+dna.pdb Info: STRUCTURE FILE pore+dna.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.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 Warning: VDW TYPE NAME NS MATCHES PARAMETER TYPE NAME N* Warning: VDW TYPE NAME NB 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 NA MATCHES PARAMETER TYPE NAME N* Info: **************************** Info: STRUCTURE SUMMARY: Info: 2015 ATOMS Info: 3093 BONDS Info: 7106 ANGLES Info: 732 DIHEDRALS Info: 45 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 1771 CONSTRAINTS Info: 6045 DEGREES OF FREEDOM Info: 1922 HYDROGEN GROUPS Info: TOTAL MASS = 37568.5 amu Info: TOTAL CHARGE = -7.00015 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 4 (PERIODIC) Info: REMOVING COM VELOCITY 0.107794 0.027103 -0.0810493 Info: LARGEST PATCH (2) HAS 1043 ATOMS Info: CREATING 476 COMPUTE OBJECTS Info: Entering startup phase 4 with 8488 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 9372 kB of memory in use. Info: Entering startup phase 6 with 9372 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 9372 kB of memory in use. Info: CREATING 476 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Entering startup phase 8 with 9372 kB of memory in use. Info: Finished startup with 9856 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: 0 495.1225 135.8713 149.5721 4.7034 -205965.4664 356.9980 730.9732 0.0000 1757.6728 -202334.5532 292.6389 -202332.1445 -202332.1445 292.6389 -12117.7888 -12156.6865 121392.7382 -12117.7888 -12156.6865 OPENING EXTENDED SYSTEM TRAJECTORY FILE Info: Initial time: 1 CPUs 0.0710673 s/step 0.822538 days/ns 18788 kB memory TIMING: 100 CPU: 7.46387, 0.0695394/step Wall: 7.87883, 0.07287/step, 0.0182175 hours remaining, 18788 kB of memory in use. ENERGY: 100 1048.9790 221.7882 168.2308 5.7399 -210500.4492 3437.8389 1472.8185 0.0000 1924.4579 -202220.5959 320.4074 -202215.8341 -202221.9439 291.7973 13728.1873 13790.4857 112676.3683 36.7935 37.4212 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 0.0583693 s/step 0.67557 days/ns 19268 kB memory TIMING: 200 CPU: 13.148, 0.0568414/step Wall: 13.8803, 0.0600149/step, 0.0133367 hours remaining, 19268 kB of memory in use. ENERGY: 200 1129.3931 215.3285 164.9319 6.7611 -206605.0830 97.0492 926.4868 0.0000 1929.4038 -202135.7286 321.2308 -202132.0020 -202132.0375 320.6681 -13511.9267 -13564.9542 119837.6990 441.3312 441.6981 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 0.0580915 s/step 0.672355 days/ns 19460 kB memory TIMING: 300 CPU: 18.8581, 0.0571013/step Wall: 19.8541, 0.0597373/step, 0.0116156 hours remaining, 19460 kB of memory in use. ENERGY: 300 1078.4809 238.7776 153.3401 8.7771 -211011.6248 4036.0156 1502.4848 0.0000 1931.3247 -202062.4239 321.5506 -202057.4190 -202061.8971 320.9066 15190.1239 15224.0424 112002.5591 188.0667 187.1581 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 0.0576631 s/step 0.667397 days/ns 19464 kB memory TIMING: 400 CPU: 24.5613, 0.0570313/step Wall: 25.7882, 0.0593416/step, 0.00989027 hours remaining, 19464 kB of memory in use. ENERGY: 400 1032.2267 227.5505 166.1161 7.7837 -206424.8354 200.9664 820.3857 0.0000 2000.9808 -201968.8254 333.1478 -201965.4095 -201963.9166 325.5134 -13450.0716 -13475.7737 118894.2436 310.7569 312.2215 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 0.057406 s/step 0.664421 days/ns 19600 kB memory TIMING: 500 CPU: 30.2014, 0.0564014/step Wall: 31.529, 0.0574076/step, 0.00797328 hours remaining, 19600 kB of memory in use. ENERGY: 500 1025.1127 255.3258 176.3028 11.3994 -211046.9822 4071.4068 1507.2288 0.0000 2053.2229 -201946.9830 341.8458 -201942.0781 -201945.2834 332.3441 15897.2856 15947.1853 110718.7961 196.9371 197.5318 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 0.0570394 s/step 0.660178 days/ns 19724 kB memory TIMING: 600 CPU: 35.8515, 0.0565014/step Wall: 37.2331, 0.0570416/step, 0.00633795 hours remaining, 19724 kB of memory in use. ENERGY: 600 983.7595 275.7236 155.4339 8.7250 -206550.9806 287.3351 853.5837 0.0000 2050.6870 -201935.7329 341.4235 -201932.8002 -201928.4357 334.1173 -13353.1340 -13387.5417 117838.6276 218.6000 218.5991 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: 41.5067, 0.0565514/step Wall: 42.9715, 0.057384/step, 0.004782 hours remaining, 19752 kB of memory in use. ENERGY: 700 1044.8552 239.1727 156.7832 8.4751 -210792.8973 3776.5872 1516.4204 0.0000 2095.6996 -201954.9038 348.9178 -201951.3302 -201948.2398 337.5210 14552.8613 14572.1623 110391.9389 229.6267 230.4718 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: 47.1608, 0.0565414/step Wall: 48.7124, 0.0574086/step, 0.00318937 hours remaining, 19752 kB of memory in use. ENERGY: 800 1105.8790 278.5126 178.8406 9.8968 -206512.5514 119.1107 830.3633 0.0000 2003.5874 -201986.3609 333.5818 -201981.7239 -201982.8016 336.2558 -13499.7112 -13513.6498 117307.9437 183.4571 183.6296 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: 52.804, 0.0564314/step Wall: 54.4287, 0.0571626/step, 0.00158785 hours remaining, 19788 kB of memory in use. ENERGY: 900 1045.8254 296.7137 194.3968 11.3309 -210697.4442 3688.6864 1501.8823 0.0000 1978.9044 -201979.7043 329.4723 -201975.8284 -201974.6092 335.5964 14204.0647 14255.5198 109940.6487 355.7072 356.0646 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: 58.3991, 0.0559515/step Wall: 60.2316, 0.058029/step, 0 hours remaining, 19788 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 1085.5568 261.9974 160.5078 7.0268 -206553.0079 252.2157 789.5599 0.0000 2076.8057 -201919.3379 345.7721 -201915.1571 -201914.7201 343.0099 -12982.0748 -13015.5567 116550.9127 157.7868 157.8454 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: 60.869072 CPUTime: 58.534100 Memory: 19788 kB