Charm++: scheduler running in netpoll mode. Info: NAMD 2.5 for Linux-i686-TCP 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 Kale et al., J. Comp. Phys. 151:283-312 (1999) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 050612 for net-linux-tcp-icc Info: Built Fri Sep 26 17:30:07 CDT 2003 by jim on santiago.ks.uiuc.edu Info: Sending usage information to NAMD developers via UDP. Sent data is: Info: 1 NAMD 2.5 Linux-i686-TCP 16 compute-0-11.local zhongwy Info: Running on 16 processors. Info: 1476 kB of memory in use. Measuring processor speeds... Done. Info: Changed directory to /home/zhongwy/namd/model1 Info: Configuration file is open4.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE /home/zhongwy/namd/model1/open04_out.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 30 Info: PERIODIC CELL BASIS 1 160.452 0 0 Info: PERIODIC CELL BASIS 2 0 160.452 0 Info: PERIODIC CELL BASIS 3 0 0 71.5922 Info: PERIODIC CELL CENTER 0 0 0 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 6000 steps Info: FIRST LDB TIMESTEP 150 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: INITIAL TEMPERATURE 310 Info: CENTER OF MASS MOVING? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME /home/zhongwy/namd/model1/open04_out.dcd Info: DCD FREQUENCY 12000 Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE Info: XST FILENAME open04_out Info: XST FREQUENCY 600 Info: VELOCITY DCD FILENAME /home/zhongwy/namd/model1/open04_out.veldcd Info: VELOCITY DCD FREQUENCY 12000 Warning: INITIAL VELOCITIES WILL NOT BE WRITTEN TO DCD FILE Info: OUTPUT FILENAME /home/zhongwy/namd/model1/open04_out Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME /home/zhongwy/namd/model1/open04_out.restart Info: RESTART FREQUENCY 500 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 8 Info: SWITCHING OFF 10 Info: PAIRLIST DISTANCE 13.5 Info: PAIRLIST SHRINK RATE 0.01 Info: PAIRLIST GROW RATE 0.01 Info: PAIRLIST TRIGGER 0.3 Info: PAIRLISTS PER CYCLE 4 Info: PAIRLISTS ENABLED Info: MARGIN 0.96 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.96 Info: ENERGY OUTPUT STEPS 60 Info: TIMING OUTPUT STEPS 60 Info: PRESSURE OUTPUT STEPS 60 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS Info: EXCLUDE FROM PRESSURE ACTIVE Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE Info: TARGET PRESSURE IS 1.01325 BAR Info: OSCILLATION PERIOD IS 240 FS Info: DECAY TIME IS 120 FS Info: PISTON TEMPERATURE IS 310 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS 2.0481e-05 2.0481e-05 -1.50037e-06 Info: CELL FLUCTUATION IS ANISOTROPIC Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-06 Info: PME EWALD COEFFICIENT 0.312341 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 160 160 80 Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686-TCP.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.5_Linux-i686-TCP.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 6 Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: RIGID BONDS TO HYDROGEN : ALL Info: ERROR TOLERANCE : 1e-08 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS Info: RANDOM NUMBER SEED 1093158944 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB /home/zhongwy/namd/model1/open04.pdb Info: STRUCTURE FILE /home/zhongwy/namd/model1/open04.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS /home/zhongwy/namd/toppar/par_all27_prot_lipid.inp Info: SUMMARY OF PARAMETERS: Info: 179 BONDS Info: 441 ANGLES Info: 534 DIHEDRAL Info: 49 IMPROPER Info: 89 VDW Info: 0 VDW_PAIRS Info: Got 14136 excluded pressure atoms.Info: **************************** Info: STRUCTURE SUMMARY: Info: 191210 ATOMS Info: 154141 BONDS Info: 191260 ANGLES Info: 216053 DIHEDRALS Info: 3150 IMPROPERS Info: 0 EXCLUSIONS Info: 158174 RIGID BONDS Info: 415456 DEGREES OF FREEDOM Info: 69678 HYDROGEN GROUPS Info: TOTAL MASS = 1.14312e+06 amu Info: TOTAL CHARGE = 6.00008 e Info: ***************************** Info: Entering startup phase 0 with 41317 kB of memory in use. Info: Entering startup phase 1 with 41316 kB of memory in use. Info: Entering startup phase 2 with 63407 kB of memory in use. Info: Entering startup phase 3 with 64903 kB of memory in use. Info: PATCH GRID IS 9 (PERIODIC) BY 9 (PERIODIC) BY 4 (PERIODIC) Info: REMOVING COM VELOCITY -0.0176036 0.0241542 0.00893976 Info: LARGEST PATCH (177) HAS 660 ATOMS Info: Entering startup phase 4 with 86879 kB of memory in use. Info: PME using 16 and 16 processors for FFT and reciprocal sum. Creating Strategy 4 Creating Strategy 4 Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Entering startup phase 5 with 87925 kB of memory in use. Info: Entering startup phase 6 with 69196 kB of memory in use. Info: Entering startup phase 7 with 69241 kB of memory in use. Info: COULOMB TABLE R-SQUARED SPACING: 0.0625 Info: COULOMB TABLE SIZE: 705 POINTS Info: NONZERO IMPRECISION IN COULOMB TABLE: 4.23516e-22 (675) 8.47033e-22 (675) Info: NONZERO IMPRECISION IN COULOMB TABLE: 5.04871e-29 (657) 1.26218e-28 (657) Info: NONZERO IMPRECISION IN COULOMB TABLE: 2.64698e-23 (701) 5.29396e-23 (701) Info: Entering startup phase 8 with 72946 kB of memory in use. Info: Finished startup with 75636 kB of memory in use. TCL: Minimizing for 300 steps PRESSURE: 0 12225.7 31.7533 -85.0977 31.7533 11755.1 -0.415589 -85.0977 -0.415589 10894 GPRESSURE: 0 -1425.74 -44.4534 -108.383 70.8073 -1705.55 12.4179 -71.5213 47.9666 -1666.46 ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 10013.3126 50545.6788 19255.1095 778.9379 -459565.0759 6972.0067 0.0000 0.0000 0.0000 -372000.0304 0.0000 -372000.0304 -372000.0304 0.0000 11624.9321 -1599.2471 1843130.0424 11624.9321 -1599.2471 INITIAL STEP: 1e-06 GRADIENT TOLERANCE: 11421.6 PRESSURE: 1 12200.3 31.9643 -84.9535 31.9643 11729.8 -0.575369 -84.9535 -0.575369 10869.5 GPRESSURE: 1 -1426.9 -44.2689 -108.301 70.9666 -1706.63 12.296 -71.4742 47.814 -1667.42 ENERGY: 1 9989.4196 50518.9176 19254.1556 778.1940 -459621.9612 6967.1133 0.0000 0.0000 0.0000 -372114.1611 0.0000 -372114.1611 -372114.1611 0.0000 11599.8881 -1600.3189 1843130.0424 11599.8881 -1600.3189 PRESSURE: 2 12174.9 32.1749 -84.8087 32.1749 11704.6 -0.736476 -84.8087 -0.736476 10845 GPRESSURE: 2 -1428.07 -44.085 -108.218 71.1253 -1707.72 12.1728 -71.4266 47.6602 -1668.39 ENERGY: 2 9965.6580 50492.1965 19253.2023 777.4507 -459678.8507 6962.2221 0.0000 0.0000 0.0000 -372228.1212 0.0000 -372228.1212 -372228.1212 0.0000 11574.8389 -1601.3922 1843130.0424 11574.8389 -1601.3922 PRESSURE: 3 12124 32.5976 -84.52 32.5976 11654.1 -1.05656 -84.52 -1.05656 10796 GPRESSURE: 3 -1430.41 -43.7156 -108.053 71.4443 -1709.89 11.9286 -71.3322 47.3546 -1670.32 ENERGY: 3 9918.5284 50438.8741 19251.2975 775.9658 -459792.6410 6952.4466 0.0000 0.0000 0.0000 -372455.5286 0.0000 -372455.5286 -372455.5286 0.0000 11524.7254 -1603.5432 1843130.0424 11524.7254 -1603.5432 BRACKET: 0.000906004 241.588 -236453 -297.301 711652 PRESSURE: 297 -5849.44 61.0328 -13.2493 61.0328 -5878.95 47.7604 -13.2493 47.7604 -5694.82 GPRESSURE: 297 -5795.02 61.2103 -15.267 60.4923 -5828.28 34.476 -14.422 43.5039 -5628.33 ENERGY: 297 16877.4086 21265.1075 14131.6531 121.7978 -588116.2125 12792.2351 0.0000 0.0000 0.0000 -522928.0105 0.0000 -522928.0105 -522928.0105 0.0000 -5807.7353 -5750.5453 1843130.0424 -5807.7353 -5750.5453 BRACKET: 0.000294172 26.7725 -236453 -297.301 70736.8 PRESSURE: 298 -5864.72 60.4689 -13.5948 60.4689 -5893.94 48.4114 -13.5948 48.4114 -5708.28 GPRESSURE: 298 -5798.13 60.7219 -15.2741 60.5084 -5831.19 34.9578 -14.5337 43.9209 -5631.92 ENERGY: 298 16876.3623 21267.3054 14133.0437 121.4172 -588086.7361 12758.2269 0.0000 0.0000 0.0000 -522930.3806 0.0000 -522930.3806 -522930.3806 0.0000 -5822.3101 -5753.7439 1843130.0424 -5822.3101 -5753.7439 BRACKET: 0.000232988 26.7725 -236453 -297.301 6804.83 PRESSURE: 299 -5866.27 60.4121 -13.6297 60.4121 -5895.46 48.4772 -13.6297 48.4772 -5709.64 GPRESSURE: 299 -5798.44 60.6726 -15.2751 60.5098 -5831.48 35.0067 -14.5451 43.9632 -5632.27 ENERGY: 299 16876.3925 21267.5834 14133.1855 121.3813 -588083.7890 12754.8466 0.0000 0.0000 0.0000 -522930.3998 0.0000 -522930.3998 -522930.3998 0.0000 -5823.7887 -5754.0632 1843130.0424 -5823.7887 -5754.0632 LDB: LOAD: AVG 187.349 MAX 222.11 MSGS: TOTAL 490 MAXC 36 MAXP 6 None LDB: LOAD: AVG 187.349 MAX 213.324 MSGS: TOTAL 490 MAXC 36 MAXP 6 Alg7 LDB: LOAD: AVG 187.349 MAX 191.096 MSGS: TOTAL 490 MAXC 36 MAXP 6 Alg7 BRACKET: 6.79814e-06 0.0191917 -297.301 412.909 6804.83 PRESSURE: 300 -5866.27 60.4121 -13.6297 60.4121 -5895.46 48.4772 -13.6297 48.4772 -5709.64 GPRESSURE: 300 -5798.44 60.6726 -15.2751 60.5098 -5831.48 35.0067 -14.5451 43.9632 -5632.27 Info: Initial time: 16 CPUs 1.58471 s/step 9.17075 days/ns 89762 kB memory TIMING: 300 CPU: 337.92, 1.17067/step Wall: 464.041, 1.67394/step, 0 hours remaining, 89762 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: 300 16876.3925 21267.5834 14133.1855 121.3813 -588083.7890 12754.8466 0.0000 0.0000 0.0000 -522930.3998 0.0000 -522930.3998 -522930.3998 0.0000 -5823.7887 -5754.0632 1843130.0424 -5823.7887 -5754.0632 REINITIALIZING VELOCITIES AT STEP 300 TO 310 KELVIN. TCL: Running for 240000 steps PRESSURE: 300 -18807.9 85.8022 -49.8962 85.8022 -18815 10.519 -49.8962 10.519 -17648.5 GPRESSURE: 300 -2417.28 54.2482 -17.006 50.3727 -2473.46 40.5361 -21.5622 49.8388 -2263.83 ENERGY: 300 1600.4176 12247.5131 14132.3422 121.3914 -538462.4120 11822.1967 0.0000 0.0000 128226.5681 -370311.9829 310.6300 -370205.9893 -370603.4650 310.6300 -18423.8146 -2384.8568 1843130.0424 -18423.8146 -2384.8568 PRESSURE: 360 -14966.8 11.218 81.4132 11.218 -15085.4 119.627 81.4132 119.627 -16025.2 GPRESSURE: 360 39.7387 -10.3614 65.9237 2.86183 -181.661 84.3108 82.4266 114.5 -1314.77 PRESSAVG: 360 -72.9703 18.6749 -47.0891 18.6749 -80.8714 43.2176 -47.0891 43.2176 57.2525 GPRESSAVG: 360 -96.3362 27.9639 -45.4721 14.6062 -103.219 40.1528 -45.5005 45.1154 40.2428 TIMING: 360 CPU: 371.03, 0.522/step Wall: 504.026, 0.625491/step, 41.689 hours remaining, 109830 kB of memory in use. ENERGY: 360 6580.3397 35853.6740 17020.2224 502.2876 -502246.1567 12015.9528 0.0000 0.0000 75679.7079 -354593.9724 183.3348 -353714.0394 -355724.2923 185.7602 -15359.1283 -485.5657 1797072.9897 -32.1964 -53.1040 PRESSURE: 420 -14635.7 -34.1125 -80.5167 -34.1125 -14843.2 -84.9487 -80.5167 -84.9487 -14496.8 GPRESSURE: 420 431.086 -87.0821 -88.64 -2.03977 214.365 -34.7191 -7.35093 -52.0766 436.119 PRESSAVG: 420 82.5132 -10.7826 -32.8258 -10.7826 22.1433 43.8931 -32.8258 43.8931 -97.1516 GPRESSAVG: 420 84.9797 -11.5285 -31.5435 -11.8713 26.3207 44.9886 -35.6428 40.4116 -95.1269 TIMING: 420 CPU: 402.07, 0.517333/step Wall: 542.367, 0.639016/step, 42.5798 hours remaining, 110380 kB of memory in use. ENERGY: 420 6670.1331 35149.6927 17316.4908 508.4572 -504676.7590 14820.4116 0.0000 0.0000 86470.6100 -343740.9636 209.4758 -342853.2116 -343918.2670 201.3009 -14658.5691 360.5233 1786480.4498 2.5016 5.3911 LDB: LOAD: AVG 85.3655 MAX 92.1302 MSGS: TOTAL 490 MAXC 36 MAXP 6 None LDB: LOAD: AVG 85.3655 MAX 87.0726 MSGS: TOTAL 490 MAXC 36 MAXP 6 Refine Info: Initial time: 16 CPUs 0.630155 s/step 3.64673 days/ns 110661 kB memory PRESSURE: 480 -14652.1 122.548 -3.35998 122.548 -14512.3 38.3155 -3.35998 38.3155 -14159 GPRESSURE: 480 266.008 111.04 -21.4092 102.096 420.701 56.0595 -45.8125 87.7705 589.423 PRESSAVG: 480 -10.6548 11.3001 23.0376 11.3001 -33.588 -14.1275 23.0376 -14.1275 -25.4233 GPRESSAVG: 480 -14.5912 11.9878 23.5066 18.4026 -36.1931 -14.6934 27.0698 -9.89237 -29.1378 TIMING: 480 CPU: 434.17, 0.535/step Wall: 581.27, 0.648395/step, 43.1939 hours remaining, 110966 kB of memory in use. ENERGY: 480 7149.9883 36804.1196 17556.3492 553.9061 -501801.5752 14528.6707 0.0000 0.0000 90965.9182 -334242.6233 220.3657 -333295.6015 -334009.1870 215.4618 -14441.1033 425.3776 1789976.2464 -23.2220 -26.6407 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 45500 WRITING COORDINATES TO RESTART FILE AT STEP 45500 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 45500 FINISHED WRITING RESTART VELOCITIES PRESSURE: 45540 -13031.5 3.75903 -77.6143 3.75903 -13135.9 95.4728 -77.6143 95.4728 -12880.8 GPRESSURE: 45540 103.131 34.2485 -78.8668 -2.49724 -140.936 160.704 9.04921 66.5082 42.4228 PRESSAVG: 45540 15.98 -46.4329 -25.015 -46.4329 24.8976 40.6393 -25.015 40.6393 11.2617 GPRESSAVG: 45540 12.7577 -43.3362 -26.4909 -46.8214 21.6968 39.2626 -18.0376 41.4199 15.8527 TIMING: 45540 CPU: 22562.2, 0.500167/step Wall: 28593.1, 0.632816/step, 34.2354 hours remaining, 133169 kB of memory in use. ENERGY: 45540 10128.7577 49913.0749 19170.9633 752.4731 -459927.9762 7415.9191 0.0000 0.0000 127232.8579 -245313.9303 308.2227 -243915.0797 -243921.9464 310.7502 -13016.0397 1.5393 1845699.9337 17.3798 16.7691 PRESSURE: 45600 -13012.1 -32.9593 -14.2789 -32.9593 -12814.4 7.8037 -14.2789 7.8037 -13020.3 GPRESSURE: 45600 76.2933 3.49502 -61.8756 -53.8462 197.872 -23.5881 44.5664 92.6392 -78.4904 PRESSAVG: 45600 27.827 -13.3355 21.8155 -13.3355 -22.8187 -33.5264 21.8155 -33.5264 36.7187 GPRESSAVG: 45600 29.1639 -10.5093 24.583 -9.39189 -22.498 -34.5971 17.7242 -34.8321 36.848 TIMING: 45600 CPU: 22592.2, 0.501667/step Wall: 28630.6, 0.625788/step, 33.8447 hours remaining, 133305 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: 45600 9881.2208 50222.0209 19136.6665 764.5627 -459865.4452 7367.0062 0.0000 0.0000 127188.1493 -245305.8187 308.1144 -243907.6924 -243906.7671 310.2825 -12948.9616 65.2249 1845657.8184 13.9090 14.5046 PRESSURE: 45660 -13380.5 -56.5093 -166.372 -56.5093 -13371.2 -140.451 -166.372 -140.451 -12859.2 GPRESSURE: 45660 -254.841 -25.7056 -149.253 -52.5796 -232.627 -175.612 -140.973 -111.688 -92.7249 PRESSAVG: 45660 -76.134 -19.4506 35.498 -19.4506 32.5954 5.48497 35.498 5.48497 10.773 GPRESSAVG: 45660 -75.8833 -16.55 37.8415 -20.5701 37.7025 6.95833 37.0597 5.93364 6.03581 TIMING: 45660 CPU: 22622.2, 0.498833/step Wall: 28667.6, 0.615844/step, 33.2966 hours remaining, 132841 kB of memory in use. ENERGY: 45660 10127.3071 50277.0751 19278.6846 737.3540 -460179.9486 7236.9940 0.0000 0.0000 127257.1833 -245265.3505 308.2816 -243869.3247 -243864.0381 310.1951 -13203.6435 -193.3977 1846962.6004 -10.9219 -10.7150 PRESSURE: 45720 -13237.7 7.48409 -1.61743 7.48409 -13107.5 -86.1827 -1.61743 -86.1827 -12636.7 GPRESSURE: 45720 -46.4111 -42.7502 9.51979 -66.075 -46.0552 -45.5292 -4.56484 12.4991 147.406 PRESSAVG: 45720 -25.4486 -19.4341 -52.6259 -19.4341 48.9222 -33.9472 -52.6259 -33.9472 2.25323 GPRESSAVG: 45720 -27.6634 -20.8698 -50.0305 -22.6624 48.123 -33.8822 -54.5265 -33.7556 2.7462 TIMING: 45720 CPU: 22651, 0.480667/step Wall: 28705.4, 0.630921/step, 34.1013 hours remaining, 133017 kB of memory in use. ENERGY: 45720 10124.9906 50114.3886 19162.2266 768.8231 -459909.0252 7556.1260 0.0000 0.0000 126998.7138 -245183.7564 307.6555 -243778.8976 -243805.7659 310.1277 -12993.9826 18.3132 1845386.9310 8.5756 7.7353 ERROR: Constraint failure in RATTLE algorithm for atom 167282! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 167291! ERROR: Constraint failure; simulation has become unstable. ERROR: Exiting prematurely. ========================================== WallClock: 28731.539760 CPUTime: 22671.870000 Memory: 132499 kB