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 null10.0.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME null10.0.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME null10.0 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME null10.0.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 1175903894 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 4102.2115 0.0000 2032.8307 -304127.0306 300.6957 -304125.2857 -304125.2857 300.6957 -132150.4079 -132150.4079 23485.4484 -132150.4079 -132150.4079 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. Info: Initial time: 1 CPUs 0.122805 s/step 1.42136 days/ns 24012 kB memory TIMING: 100 CPU: 14.3088, 0.121781/step Wall: 14.7291, 0.124457/step, 0.0311141 hours remaining, 24012 kB of memory in use. ENERGY: 100 20.7461 0.4008 0.0000 0.0000 -307300.7989 -1870.2697 1712.7138 0.0000 3242.9034 -304194.3046 479.6894 -304192.2097 -304193.3063 501.9921 -121203.6697 -121203.6697 23485.4484 -127641.5593 -127641.5593 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 0.118861 s/step 1.37571 days/ns 24508 kB memory TIMING: 200 CPU: 26.019, 0.117102/step Wall: 26.7808, 0.120518/step, 0.0267817 hours remaining, 24508 kB of memory in use. ENERGY: 200 24.6816 0.4355 0.0000 0.0000 -307784.2284 -2152.3013 2320.9533 0.0000 3352.0264 -304238.4329 495.8308 -304236.5329 -304236.6850 452.5737 -124055.2645 -124055.2645 23485.4484 -123734.3769 -123734.3769 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 0.118161 s/step 1.3676 days/ns 24508 kB memory TIMING: 300 CPU: 37.5663, 0.115472/step Wall: 38.762, 0.119812/step, 0.0232967 hours remaining, 24508 kB of memory in use. ENERGY: 300 26.6729 0.4867 0.0000 0.0000 -307418.8405 -2057.8371 2244.8528 0.0000 2922.5867 -304282.0786 432.3082 -304280.3561 -304279.5616 476.9172 -129557.2978 -129557.2978 23485.4484 -125878.8711 -125878.8711 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 0.120736 s/step 1.3974 days/ns 24508 kB memory TIMING: 400 CPU: 49.4315, 0.118652/step Wall: 51.0002, 0.122382/step, 0.0203969 hours remaining, 24508 kB of memory in use. ENERGY: 400 24.3535 0.4490 0.0000 0.0000 -307736.7714 -2013.4896 2232.6603 0.0000 3172.6643 -304320.1340 469.2996 -304318.3429 -304317.6356 471.9075 -121315.9848 -121315.9848 23485.4484 -125732.0281 -125732.0281 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 0.118493 s/step 1.37144 days/ns 24508 kB memory TIMING: 500 CPU: 60.9927, 0.115612/step Wall: 62.8496, 0.118494/step, 0.0164575 hours remaining, 24508 kB of memory in use. ENERGY: 500 23.9708 0.4232 0.0000 0.0000 -307443.1707 -2033.0207 1925.0358 0.0000 3178.6457 -304348.1159 470.1844 -304345.7883 -304347.0570 454.5293 -125973.0192 -125973.0192 23485.4484 -122337.2498 -122337.2498 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 0.121073 s/step 1.4013 days/ns 24508 kB memory TIMING: 600 CPU: 72.7479, 0.117552/step Wall: 74.9574, 0.121078/step, 0.0134531 hours remaining, 24508 kB of memory in use. ENERGY: 600 24.3318 0.4498 0.0000 0.0000 -307643.1129 -2022.9286 2309.9346 0.0000 2942.1412 -304389.1842 435.2007 -304387.0019 -304387.4620 462.7036 -125977.3319 -125977.3319 23485.4484 -126455.4928 -126455.4928 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: 84.0672, 0.113193/step Wall: 86.678, 0.117207/step, 0.00976721 hours remaining, 24508 kB of memory in use. ENERGY: 700 23.3769 0.4286 0.0000 0.0000 -307467.5825 -2070.3361 1912.5135 0.0000 3155.4820 -304446.1176 466.7580 -304443.8281 -304444.5780 458.3842 -122727.5856 -122727.5856 23485.4484 -122228.6513 -122228.6513 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: 96.0104, 0.119432/step Wall: 98.8959, 0.122178/step, 0.00678769 hours remaining, 24508 kB of memory in use. ENERGY: 800 22.8978 0.4265 0.0000 0.0000 -307656.4546 -2056.2368 2039.4941 0.0000 3169.1991 -304480.6739 468.7870 -304478.6379 -304478.6029 448.7276 -126279.7454 -126279.7454 23485.4484 -124263.1644 -124263.1644 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: 107.265, 0.112543/step Wall: 110.378, 0.11482/step, 0.00318945 hours remaining, 24508 kB of memory in use. ENERGY: 900 23.3790 0.4277 0.0000 0.0000 -307563.0684 -2022.9600 1980.0774 0.0000 3051.9193 -304530.2251 451.4390 -304528.0582 -304528.2426 452.9414 -123518.2277 -123518.2277 23485.4484 -125205.1882 -125205.1882 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: 118.763, 0.114983/step Wall: 122.21, 0.11832/step, 0 hours remaining, 24508 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 23.3506 0.4320 0.0000 0.0000 -307576.2080 -2040.9447 1979.5303 0.0000 3054.0412 -304559.7986 451.7529 -304557.4790 -304558.4511 446.6362 -123255.3722 -123255.3722 23485.4484 -122521.7936 -122521.7936 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: 123.348877 CPUTime: 119.137886 Memory: 24508 kB