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 33.2024 19.167 0 Info: PERIODIC CELL BASIS 2 0 38.3342 0 Info: PERIODIC CELL BASIS 3 0 0 64.8282 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, 7.1096) Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 295 Info: LANGEVIN DAMPING COEFFICIENTS DETERMINED FROM FILES Info: LANGEVIN DAMPING FILE: sample1.0.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 1163416320 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB sample.pdb Info: STRUCTURE FILE sample.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 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: 7832 ATOMS Info: 6869 BONDS Info: 8994 ANGLES Info: 732 DIHEDRALS Info: 45 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 1758 CONSTRAINTS Info: 23496 DEGREES OF FREEDOM Info: 3963 HYDROGEN GROUPS Info: TOTAL MASS = 77297.6 amu Info: TOTAL CHARGE = -0.000154442 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 8232 kB of memory in use. Info: Entering startup phase 3 with 8232 kB of memory in use. Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 3 (PERIODIC) Info: REMOVING COM VELOCITY 0.0334506 0.076552 -0.0372347 Info: LARGEST PATCH (0) HAS 2801 ATOMS Info: CREATING 957 COMPUTE OBJECTS Info: Entering startup phase 4 with 9584 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 10776 kB of memory in use. Info: Entering startup phase 6 with 10776 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 10776 kB of memory in use. Info: CREATING 957 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Entering startup phase 8 with 11132 kB of memory in use. Info: Finished startup with 11644 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 2629.6381 964.6770 149.9487 2.8053 -247574.1217 5353.0356 1044.3590 -621.7997 6856.9969 -231194.4608 293.7179 -231091.4783 -231091.4783 293.7179 2888.8928 330.1234 82512.5189 2888.8928 330.1234 OPENING EXTENDED SYSTEM TRAJECTORY FILE Info: Initial time: 1 CPUs 0.231052 s/step 2.67421 days/ns 40748 kB memory TIMING: 100 CPU: 25.0872, 0.228845/step Wall: 25.5492, 0.232705/step, 0.0581762 hours remaining, 40748 kB of memory in use. ENERGY: 100 2765.0830 1032.5122 145.4385 9.5025 -246398.6752 5492.9759 1085.1214 -2960.2246 7620.4580 -231207.8084 326.4206 -231107.5897 -231102.3053 313.6890 3780.8754 1351.7348 82512.5189 1658.0359 1654.8494 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 0.22919 s/step 2.65266 days/ns 42500 kB memory TIMING: 200 CPU: 47.7557, 0.226686/step Wall: 48.6172, 0.23068/step, 0.0512623 hours remaining, 42500 kB of memory in use. ENERGY: 200 2834.4859 1031.2397 150.4610 6.0409 -245671.3232 5544.3316 1110.7517 -4133.7157 7903.8019 -231223.9263 338.5575 -231125.8770 -231115.5645 330.6664 3364.8115 1613.5764 82512.5189 1603.1906 1606.0567 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 0.22955 s/step 2.65683 days/ns 42868 kB memory TIMING: 300 CPU: 70.3043, 0.225486/step Wall: 71.7273, 0.231101/step, 0.0449363 hours remaining, 42868 kB of memory in use. ENERGY: 300 2899.6142 1027.7373 168.4638 5.8604 -245528.3774 5847.6425 1121.2824 -5049.7440 8270.3199 -231237.2009 354.2573 -231137.4261 -231137.1587 345.4259 5963.5818 4021.8615 82512.5189 2831.7225 2834.8943 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 0.224716 s/step 2.60088 days/ns 43388 kB memory TIMING: 400 CPU: 92.5399, 0.222356/step Wall: 94.3725, 0.226452/step, 0.037742 hours remaining, 43388 kB of memory in use. ENERGY: 400 2870.4756 1087.5408 157.8755 5.5504 -245135.6070 5806.3271 1152.8967 -5677.0347 8438.8265 -231293.1490 361.4752 -231194.7547 -231191.8997 356.6416 6532.5554 4211.5669 82512.5189 4445.7746 4440.9849 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 0.227568 s/step 2.63389 days/ns 43772 kB memory TIMING: 500 CPU: 114.789, 0.222486/step Wall: 117.13, 0.227572/step, 0.0316072 hours remaining, 43772 kB of memory in use. ENERGY: 500 2881.2074 1089.9515 160.9172 5.4979 -244884.6386 5889.5514 1173.8111 -6280.2095 8642.0489 -231321.8627 370.1802 -231223.3835 -231221.4148 365.2489 6424.1641 4169.5683 82512.5189 4116.3191 4113.8889 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 0.224319 s/step 2.59628 days/ns 44528 kB memory TIMING: 600 CPU: 136.921, 0.221326/step Wall: 139.562, 0.224323/step, 0.0249248 hours remaining, 44528 kB of memory in use. ENERGY: 600 2948.5607 1072.2151 167.8712 5.3589 -244800.2387 5953.9143 1238.8779 -6871.5786 8925.8230 -231359.1962 382.3356 -231259.2847 -231262.9332 374.8490 6883.6035 4800.9778 82512.5189 4485.9844 4484.9509 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: 159.077, 0.221556/step Wall: 162.697, 0.231351/step, 0.0192793 hours remaining, 44704 kB of memory in use. ENERGY: 700 2916.4494 1088.8175 158.0120 5.0651 -244594.9596 6075.5366 1192.9223 -7222.1622 8916.8909 -231463.4280 381.9530 -231366.3842 -231362.6280 380.2145 7309.4128 5096.2845 82512.5189 4843.2149 4841.0508 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: 181.221, 0.221446/step Wall: 185.021, 0.223244/step, 0.0124024 hours remaining, 44876 kB of memory in use. ENERGY: 800 2934.4005 1101.4757 154.1134 6.9893 -244326.8831 5968.0636 1232.7332 -7566.8135 9026.8004 -231469.1204 386.6609 -231369.7035 -231376.7572 383.3273 8010.4984 5484.8956 82512.5189 5280.9303 5275.7166 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: 203.696, 0.224746/step Wall: 209.31, 0.242888/step, 0.00674689 hours remaining, 45044 kB of memory in use. ENERGY: 900 2966.8709 1068.4896 162.3833 7.1884 -244129.3475 5888.3542 1227.1957 -7914.0142 9218.2479 -231504.6318 394.8615 -231406.6715 -231408.1412 389.1559 7275.9437 5184.8767 82512.5189 5363.9716 5358.1687 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: 225.946, 0.222496/step Wall: 232.1, 0.227896/step, 0 hours remaining, 45320 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 3023.0763 1087.7549 151.3549 6.1848 -244002.2221 5946.9539 1220.3084 -8273.0745 9236.4389 -231603.2245 395.6407 -231507.7905 -231500.9174 394.4275 7276.4289 5862.1868 82512.5189 5700.1970 5705.8720 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: 233.178802 CPUTime: 226.320587 Memory: 45320 kB