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 field1.0.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME field1.0.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME field1.0 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME field1.0.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 1175903593 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 410.2212 -18.8872 2032.8307 -307837.9082 300.6957 -307836.3063 -307836.3063 300.6957 -123906.6113 -123906.6113 23485.4484 -123906.6113 -123906.6113 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. 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 0.134083 s/step 1.55189 days/ns 24232 kB memory TIMING: 100 CPU: 14.0329, 0.117822/step Wall: 16.0202, 0.135802/step, 0.0339506 hours remaining, 24232 kB of memory in use. ENERGY: 100 87.3718 1.3173 0.0000 0.0000 -309921.2513 2289.4759 677.6372 -3982.1631 2969.5702 -307878.0420 439.2580 -307875.0454 -307876.9132 433.8960 -57752.7273 -57752.7273 23485.4484 -87348.1862 -87348.1862 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. 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. 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 0.131286 s/step 1.51951 days/ns 24788 kB memory TIMING: 200 CPU: 26.097, 0.120642/step Wall: 29.2947, 0.132745/step, 0.0294988 hours remaining, 24788 kB of memory in use. ENERGY: 200 143.4486 2.5902 0.0000 0.0000 -312204.0025 5392.3361 1093.7790 -6016.0621 3650.8389 -307937.0717 540.0311 -307933.0809 -307935.3423 499.6103 -12543.9485 -12543.9485 23485.4484 -25576.0153 -25576.0153 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 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. 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 0.124191 s/step 1.4374 days/ns 24864 kB memory TIMING: 300 CPU: 38.3132, 0.122161/step Wall: 41.8786, 0.125839/step, 0.0244687 hours remaining, 24864 kB of memory in use. ENERGY: 300 208.5178 4.3062 0.0000 0.0000 -314426.7121 7008.2849 1899.3281 -7350.4455 4506.9913 -308149.7293 666.6729 -308145.6793 -308145.9365 619.8753 11945.3974 11945.3974 23485.4484 -1468.2637 -1468.2637 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 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. 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: Benchmark time: 1 CPUs 0.125752 s/step 1.45547 days/ns 25008 kB memory TIMING: 400 CPU: 50.6413, 0.123281/step Wall: 54.6188, 0.127402/step, 0.0212337 hours remaining, 25008 kB of memory in use. ENERGY: 400 296.0894 5.7286 0.0000 0.0000 -317261.8561 9793.6257 2694.9992 -9323.6918 5179.7332 -308615.3718 766.1847 -308609.7959 -308612.1838 725.2317 53359.3394 53359.3394 23485.4484 35403.6358 35403.6358 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. 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. 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: Benchmark time: 1 CPUs 0.123885 s/step 1.43386 days/ns 25084 kB memory TIMING: 500 CPU: 62.8254, 0.121841/step Wall: 67.0074, 0.123886/step, 0.0172064 hours remaining, 25084 kB of memory in use. ENERGY: 500 351.5733 6.5325 0.0000 0.0000 -318252.4099 10837.0515 3199.7560 -10527.8559 5550.1574 -308835.1951 820.9777 -308828.7309 -308830.9120 802.7185 69143.4677 69143.4677 23485.4484 62690.9655 62690.9655 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. 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. 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: Benchmark time: 1 CPUs 0.124288 s/step 1.43852 days/ns 25100 kB memory TIMING: 600 CPU: 75.0306, 0.122051/step Wall: 79.4363, 0.124289/step, 0.0138099 hours remaining, 25100 kB of memory in use. ENERGY: 600 398.1278 7.0355 0.0000 0.0000 -319687.7822 11858.5383 3533.8080 -11322.0049 5982.4260 -309229.8514 884.9188 -309222.9682 -309223.8021 846.7146 84942.9129 84942.9129 23485.4484 77764.1616 77764.1616 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 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. 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. TIMING: 700 CPU: 87.5207, 0.124901/step Wall: 92.1854, 0.12749/step, 0.0106242 hours remaining, 25144 kB of memory in use. ENERGY: 700 436.6690 7.4631 0.0000 0.0000 -320554.7083 12549.8830 3771.7799 -11918.3751 6210.5632 -309496.7252 918.6648 -309489.5839 -309489.5241 899.5282 96061.0117 96061.0117 23485.4484 91024.2053 91024.2053 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 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. 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. TIMING: 800 CPU: 99.7028, 0.121821/step Wall: 104.621, 0.124361/step, 0.00690893 hours remaining, 25144 kB of memory in use. ENERGY: 800 476.7179 7.8388 0.0000 0.0000 -321180.0853 12986.8772 4030.1585 -12449.8868 6287.1013 -309841.2783 929.9863 -309832.5563 -309836.1763 938.2656 103015.3672 103015.3672 23485.4484 99193.9797 99193.9797 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 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. 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. TIMING: 900 CPU: 112.107, 0.124041/step Wall: 117.213, 0.125916/step, 0.00349767 hours remaining, 25144 kB of memory in use. ENERGY: 900 521.2481 8.1894 0.0000 0.0000 -322017.9634 13314.8372 4308.7564 -12773.8563 6466.1507 -310172.6379 956.4712 -310163.8297 -310166.0919 949.2029 108312.1432 108312.1432 23485.4484 106337.6394 106337.6394 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 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. 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. TIMING: 1000 CPU: 124.302, 0.121951/step Wall: 129.654, 0.12441/step, 0 hours remaining, 25144 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 556.2722 8.4639 0.0000 0.0000 -322587.0733 13714.5764 4544.7622 -13254.5912 6715.3568 -310302.2330 993.3337 -310293.1348 -310294.2302 968.0507 114012.6410 114012.6410 23485.4484 113289.6605 113289.6605 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: 130.724380 CPUTime: 124.615059 Memory: 25144 kB