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 tashkent.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 field.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE eq2.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 17.412 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 eq2.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 field10.0.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME field10.0.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME field10.0 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME field10.0.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, 16) Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 295 Info: LANGEVIN DAMPING COEFFICIENT IS 0.2 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS 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 48 128 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 1175904033 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ../1_build/membrane_hex.pdb Info: STRUCTURE FILE ../1_build/membrane_hex.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_silicon_ions_NEW0.1.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES eq2.coor Info: SUMMARY OF PARAMETERS: Info: 11 BONDS Info: 36 ANGLES Info: 0 DIHEDRAL Info: 0 IMPROPER Info: 0 CROSSTERM Info: 15 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 2268 ATOMS Info: 3888 BONDS Info: 9720 ANGLES Info: 0 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 2268 CONSTRAINTS Info: 6804 DEGREES OF FREEDOM Info: 2268 HYDROGEN GROUPS Info: TOTAL MASS = 45452.2 amu Info: TOTAL CHARGE = 3.86238e-05 e Info: ***************************** Info: Entering startup phase 0 with 8776 kB of memory in use. Info: Entering startup phase 1 with 8776 kB of memory in use. Info: Entering startup phase 2 with 8776 kB of memory in use. Info: Entering startup phase 3 with 8776 kB of memory in use. Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 1 (PERIODIC) Info: REMOVING COM VELOCITY -0.0118078 0.013194 -0.0196803 Info: LARGEST PATCH (0) HAS 2268 ATOMS Info: CREATING 323 COMPUTE OBJECTS Info: Entering startup phase 4 with 8776 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 10264 kB of memory in use. Info: Entering startup phase 6 with 10264 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 10264 kB of memory in use. Info: CREATING 323 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Entering startup phase 8 with 10452 kB of memory in use. Info: Finished startup with 10708 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 47.1228 0.8379 0.0000 0.0000 -308186.0814 -2123.9522 4102.2115 -18.8872 2032.8307 -304145.9178 300.6957 -304143.9391 -304143.9391 300.6957 -132130.3936 -132130.3936 23485.4484 -132130.3936 -132130.3936 OPENING EXTENDED SYSTEM TRAJECTORY FILE Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Info: Initial time: 1 CPUs 0.119893 s/step 1.38765 days/ns 24092 kB memory TIMING: 100 CPU: 13.5029, 0.119202/step Wall: 13.8333, 0.121562/step, 0.0303905 hours remaining, 24092 kB of memory in use. ENERGY: 100 25.8059 0.4771 0.0000 0.0000 -307657.9392 -171.1539 2090.5496 -1934.8515 3426.0972 -304221.0148 506.7873 -304218.2047 -304218.9463 571.7207 -86187.7018 -86187.7018 23485.4484 -100058.4131 -100058.4131 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 Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Info: Initial time: 1 CPUs 0.116512 s/step 1.34852 days/ns 24640 kB memory TIMING: 200 CPU: 24.9342, 0.114313/step Wall: 25.6492, 0.118159/step, 0.0262576 hours remaining, 24640 kB of memory in use. ENERGY: 200 29.5986 0.5279 0.0000 0.0000 -308090.6728 -831.0346 2675.6169 -1657.4703 3610.8903 -304262.5439 534.1219 -304260.0690 -304259.4482 528.7189 -104322.3778 -104322.3778 23485.4484 -94946.6124 -94946.6124 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 0.11968 s/step 1.38519 days/ns 24640 kB memory TIMING: 300 CPU: 36.6614, 0.117272/step Wall: 37.7818, 0.121325/step, 0.023591 hours remaining, 24640 kB of memory in use. ENERGY: 300 30.4608 0.5953 0.0000 0.0000 -307643.2782 -445.0662 2556.5740 -2204.4477 3385.2021 -304319.9600 500.7382 -304317.0859 -304317.1925 555.4760 -98571.1439 -98571.1439 23485.4484 -99616.7857 -99616.7857 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 0.12205 s/step 1.41261 days/ns 24640 kB memory TIMING: 400 CPU: 48.6616, 0.120002/step Wall: 50.1511, 0.123694/step, 0.0206156 hours remaining, 24640 kB of memory in use. ENERGY: 400 28.5654 0.5235 0.0000 0.0000 -308145.1669 -640.7056 2525.6919 -1756.5331 3620.9955 -304366.6293 535.6166 -304364.0933 -304363.0450 539.7432 -99786.0362 -99786.0362 23485.4484 -96750.1457 -96750.1457 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 Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Info: Benchmark time: 1 CPUs 0.11501 s/step 1.33114 days/ns 24640 kB memory TIMING: 500 CPU: 59.9739, 0.113123/step Wall: 61.6522, 0.115011/step, 0.0159737 hours remaining, 24640 kB of memory in use. ENERGY: 500 31.9819 0.5783 0.0000 0.0000 -308016.2343 -63.9018 2595.6195 -2518.6188 3565.0514 -304405.5236 527.3414 -304402.6676 -304402.6129 533.7787 -95110.2511 -95110.2511 23485.4484 -101240.5192 -101240.5192 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 Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Info: Benchmark time: 1 CPUs 0.117763 s/step 1.363 days/ns 24640 kB memory TIMING: 600 CPU: 71.4821, 0.115083/step Wall: 73.4287, 0.117765/step, 0.0130849 hours remaining, 24640 kB of memory in use. ENERGY: 600 28.9828 0.5477 0.0000 0.0000 -307955.7844 -869.0211 2520.9584 -1618.6861 3428.0495 -304464.9532 507.0761 -304461.9159 -304462.6321 538.4250 -107507.5344 -107507.5344 23485.4484 -95519.8652 -95519.8652 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: 83.2613, 0.117792/step Wall: 85.4267, 0.119981/step, 0.00999838 hours remaining, 24640 kB of memory in use. ENERGY: 700 31.0950 0.5716 0.0000 0.0000 -308277.5142 307.3884 2484.0848 -2645.6524 3585.3498 -304514.6769 530.3439 -304511.7030 -304512.1347 527.7301 -84556.9185 -84556.9185 23485.4484 -100501.6497 -100501.6497 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: 94.6126, 0.113513/step Wall: 97.0948, 0.11668/step, 0.00648224 hours remaining, 24640 kB of memory in use. ENERGY: 800 28.3580 0.5246 0.0000 0.0000 -307968.8092 -599.3770 2307.5078 -1881.4178 3524.3948 -304588.8188 521.3275 -304585.9501 -304585.7858 519.0652 -104437.6353 -104437.6353 23485.4484 -93506.8593 -93506.8593 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: 105.873, 0.112603/step Wall: 108.568, 0.114728/step, 0.00318689 hours remaining, 24640 kB of memory in use. ENERGY: 900 29.8340 0.5722 0.0000 0.0000 -308014.6449 -406.2114 2571.3783 -2272.1292 3448.9561 -304642.2450 510.1686 -304639.5081 -304638.6979 522.9163 -98188.9366 -98188.9366 23485.4484 -103123.8098 -103123.8098 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: 117.102, 0.112293/step Wall: 120.21, 0.116424/step, 0 hours remaining, 24640 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 28.4184 0.5186 0.0000 0.0000 -308000.2433 -525.5607 2293.3081 -1916.6212 3403.5238 -304716.6562 503.4483 -304714.1846 -304712.5621 510.8290 -100604.0599 -100604.0599 23485.4484 -97994.9206 -97994.9206 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: 121.239571 CPUTime: 117.353157 Memory: 24640 kB