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 null.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 null1.0.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME null1.0.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME null1.0 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME null1.0.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: 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 1175903744 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 322 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 322 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 410.2212 0.0000 2032.8307 -307819.0210 300.6957 -307817.6572 -307817.6572 300.6957 -123926.6511 -123926.6511 23485.4484 -123926.6511 -123926.6511 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. 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 0.127726 s/step 1.47831 days/ns 24076 kB memory TIMING: 100 CPU: 14.1988, 0.126241/step Wall: 14.6429, 0.129373/step, 0.0323432 hours remaining, 24076 kB of memory in use. ENERGY: 100 45.1669 0.8086 0.0000 0.0000 -308121.5602 -2214.7986 418.7619 0.0000 2060.9279 -307810.6935 304.8519 -307809.3265 -307809.3713 303.5563 -124735.0690 -124735.0690 23485.4484 -124649.0840 -124649.0840 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. Info: Initial time: 1 CPUs 0.11403 s/step 1.3198 days/ns 24588 kB memory TIMING: 200 CPU: 25.3911, 0.111923/step Wall: 26.1953, 0.115524/step, 0.0256721 hours remaining, 24588 kB of memory in use. ENERGY: 200 46.3572 0.8079 0.0000 0.0000 -308081.8748 -2225.3716 404.4465 0.0000 2042.0233 -307813.6115 302.0555 -307812.2345 -307812.1933 302.9829 -124947.5040 -124947.5040 23485.4484 -124930.5803 -124930.5803 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 0.116978 s/step 1.35391 days/ns 24588 kB memory TIMING: 300 CPU: 36.0715, 0.106804/step Wall: 38.0579, 0.118626/step, 0.0230662 hours remaining, 24588 kB of memory in use. ENERGY: 300 45.6901 0.8291 0.0000 0.0000 -308174.9757 -2182.5311 411.4680 0.0000 2086.7584 -307812.7612 308.6727 -307811.4335 -307811.2805 304.3811 -124209.3493 -124209.3493 23485.4484 -124398.6771 -124398.6771 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 0.12189 s/step 1.41076 days/ns 24588 kB memory TIMING: 400 CPU: 47.8927, 0.118212/step Wall: 50.4117, 0.123537/step, 0.0205896 hours remaining, 24588 kB of memory in use. ENERGY: 400 47.1331 0.8537 0.0000 0.0000 -308135.8726 -2194.7559 422.0376 0.0000 2055.9544 -307804.6496 304.1162 -307803.1136 -307803.8233 306.3697 -125268.4611 -125268.4611 23485.4484 -124786.5215 -124786.5215 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 0.121151 s/step 1.40221 days/ns 24588 kB memory TIMING: 500 CPU: 59.7509, 0.118582/step Wall: 62.5269, 0.121152/step, 0.0168267 hours remaining, 24588 kB of memory in use. ENERGY: 500 47.7849 0.8269 0.0000 0.0000 -308156.8965 -2157.1025 422.4792 0.0000 2041.6266 -307801.2814 301.9968 -307799.7409 -307800.4160 303.7416 -125350.3951 -125350.3951 23485.4484 -125648.2745 -125648.2745 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 0.11572 s/step 1.33935 days/ns 24652 kB memory TIMING: 600 CPU: 71.0212, 0.112703/step Wall: 74.0991, 0.115723/step, 0.0128581 hours remaining, 24652 kB of memory in use. ENERGY: 600 46.8457 0.8401 0.0000 0.0000 -308141.3626 -2153.9618 418.3693 0.0000 2020.6695 -307808.5998 298.8969 -307806.9082 -307807.9970 305.2308 -124391.9689 -124391.9689 23485.4484 -124889.0865 -124889.0865 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: 82.1725, 0.111513/step Wall: 85.4675, 0.113684/step, 0.00947363 hours remaining, 24660 kB of memory in use. ENERGY: 700 44.6576 0.8110 0.0000 0.0000 -308164.9663 -2159.0579 402.0796 0.0000 2060.4444 -307816.0317 304.7804 -307814.5536 -307814.7682 304.3657 -123616.5871 -123616.5871 23485.4484 -123823.4688 -123823.4688 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: 93.7797, 0.116072/step Wall: 97.269, 0.118015/step, 0.00655641 hours remaining, 24668 kB of memory in use. ENERGY: 800 47.1084 0.8319 0.0000 0.0000 -308205.1663 -2145.8897 422.6786 0.0000 2076.6060 -307803.8311 307.1710 -307802.3929 -307802.6743 303.9665 -123264.0029 -123264.0029 23485.4484 -123409.7954 -123409.7954 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: 105.298, 0.115182/step Wall: 108.984, 0.117151/step, 0.00325419 hours remaining, 24668 kB of memory in use. ENERGY: 900 46.6622 0.8287 0.0000 0.0000 -308154.3972 -2187.3592 418.9315 0.0000 2065.7162 -307809.6178 305.5602 -307808.1043 -307808.5155 303.3258 -124570.3348 -124570.3348 23485.4484 -123354.6330 -123354.6330 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: 116.686, 0.113883/step Wall: 120.645, 0.116605/step, 0 hours remaining, 24668 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 45.7623 0.8334 0.0000 0.0000 -308143.9706 -2149.9180 414.5013 0.0000 2023.1243 -307809.6673 299.2600 -307808.5272 -307807.6474 305.7999 -124804.0841 -124804.0841 23485.4484 -125061.2864 -125061.2864 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: 121.690704 CPUTime: 117.006210 Memory: 24668 kB