Charmrun> started all node programs in 6.406 seconds. Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'. Charm++> scheduler running in netpoll mode. CharmLB> Load balancer assumes all CPUs are same. Charm++> cpu affinity enabled. Charm++> Running on 2 unique compute nodes (4-way SMP). Charm++> cpu topology info is gathered in 0.017 seconds. Info: NAMD CVS-2011-11-20 for Linux-x86_64 Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: for updates, documentation, and support information. 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 60303 for net-linux-x86_64-iccstatic Info: Built Sun Nov 20 02:18:14 CST 2011 by jim on lisboa.ks.uiuc.edu Info: 1 NAMD CVS-2011-11-20 Linux-x86_64 8 n0007 glykos Info: Running on 8 processors, 8 nodes, 2 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0351219 s Info: 1.63499 MB of memory in use based on CmiMemoryUsage Info: Configuration file is equi.namd Info: Working in the current directory /home/glykos/tmp TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE heat_out.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 9710000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 38.6131 0 0 Info: PERIODIC CELL BASIS 2 0 38.6131 0 Info: PERIODIC CELL BASIS 3 0 0 38.6131 Info: PERIODIC CELL CENTER 0 0 0 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER. Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: MIN ATOMS PER PATCH 40 Info: VELOCITY FILE heat_out.vel Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 ELECTROSTATICS SCALED BY 0.833333 Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED Info: DCD FILENAME output/equi_out.dcd Info: DCD FREQUENCY 400 Info: DCD FIRST STEP 9710400 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME output/equi_out.xst Info: XST FREQUENCY 400 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME output/equi_out Info: RESTART FILENAME output/restart Info: RESTART FREQUENCY 10000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 7 Info: SWITCHING OFF 8 Info: PAIRLIST DISTANCE 9 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 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 11.5 Info: ENERGY OUTPUT STEPS 400 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1600 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 320 Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Info: ADAPTIVE TEMPERING ACTIVE: Info: OUTPUT FREQUENCY: 400 Info: TEMPERATURE UPDATE FREQUENCY: 10 Info: ADAPTIVE TEMPERING WILL BE DONE FROM STEP 0 Info: ADAPTIVE TEMPERING COUPLED TO LANGEVIN THERMOSTAT Info: WRITING RESTART INFORMATION TO output/restart.tempering EVERY 10000 STEPS Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-06 Info: PME EWALD COEFFICIENT 0.39467 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 40 40 40 Info: PME MAXIMUM GRID SPACING 1.5 Info: Attempting to read FFTW data from FFTW_NAMD_CVS-2011-11-20_Linux-x86_64.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_CVS-2011-11-20_Linux-x86_64.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2 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: RANDOM NUMBER SEED 1321786730 Info: USE HYDROGEN BONDS? NO Info: Using AMBER format force field! Info: AMBER PARM FILE lyta.prmtop Info: COORDINATE PDB heat_out.coor Info: Exclusions will be read from PARM file! Info: SCNB (VDW SCALING) 2 Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: FIRST TIMESTEP 9710000 Reading parm file (lyta.prmtop) ... PARM file in AMBER 7 format Warning: Encounter 10-12 H-bond term Warning: Found 1749 H-H bonds. Info: SUMMARY OF PARAMETERS: Info: 35 BONDS Info: 69 ANGLES Info: 47 DIHEDRAL Info: 0 IMPROPER Info: 0 CROSSTERM Info: 0 VDW Info: 120 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PDB FILE: 0.013526 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 5493 ATOMS Info: 5496 BONDS Info: 441 ANGLES Info: 930 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 6571 EXCLUSIONS Info: 5360 RIGID BONDS Info: 11119 DEGREES OF FREEDOM Info: 1882 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 1882 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 33380.9 amu Info: TOTAL CHARGE = -5.06639e-07 e Info: MASS DENSITY = 0.962839 g/cm^3 Info: ATOM DENSITY = 0.0954126 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 0.086426 s, 3.43864 MB of memory in use Info: Startup phase 0 took 0.00271606 s, 3.43361 MB of memory in use Info: Startup phase 1 took 0.190986 s, 4.23586 MB of memory in use Info: Startup phase 2 took 0.000653028 s, 4.31133 MB of memory in use Info: Startup phase 3 took 0.000413895 s, 4.31053 MB of memory in use Info: PATCH GRID IS 3 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: REMOVING COM VELOCITY -0.0248427 -0.0240043 0.0215009 Info: LARGEST PATCH (22) HAS 221 ATOMS Info: Startup phase 4 took 0.0176501 s, 5.31798 MB of memory in use Info: PME using 8 and 8 processors for FFT and reciprocal sum. Info: PME USING 8 GRID NODES AND 8 TRANS NODES Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 5 took 0.00163507 s, 5.38118 MB of memory in use Info: Startup phase 6 took 0.0207279 s, 4.58821 MB of memory in use LDB: Central LB being created... Info: Startup phase 7 took 0.00167704 s, 4.60774 MB of memory in use Info: CREATING 561 COMPUTE OBJECTS Info: useSync: 1 useProxySync: 0 Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 705 POINTS Info: Startup phase 8 took 0.0031991 s, 5.23363 MB of memory in use Info: Startup phase 9 took 0.000159979 s, 5.73845 MB of memory in use Info: Finished startup at 0.326244 s, 5.73845 MB of memory in use TCL: Running for 500000000 steps Info: INITIALISING ADAPTIVE TEMPERING Info: ADAPTIVE TEMPERING: TEMPERATURE RANGE: [293,600] KELVIN Info: ADAPTIVE TEMPERING: NUMBER OF BINS TO STORE POT. ENERGY: 1000 Info: ADAPTIVE TEMPERING: ADAPTIVE BIN AVERAGING PARAMETER: 0.1 Info: ADAPTIVE TEMPERING: SCALING CONSTANT FOR LANGEVIN TEMPERATURE UPDATES: 0.0001 Info: ADAPTIVE TEMPERING: INITIAL TEMPERATURE: 446.5 ENERGY: 9710000 58.4057 119.4488 143.2271 0.0000 -19534.6357 2548.7539 0.0000 0.0000 3493.1386 -13171.6616 316.1844 -16664.8002 -13161.9661 316.1844 -88.5673 26.8362 57571.0313 -88.5673 26.8362 OPENING EXTENDED SYSTEM TRAJECTORY FILE LDB: ============= START OF LOAD BALANCING ============== 0.529305 LDB: ============== END OF LOAD BALANCING =============== 0.529849 LDB: =============== DONE WITH MIGRATION ================ 0.531757 LDB: ============= START OF LOAD BALANCING ============== 1.18816 LDB: Largest compute 18 load 0.038392 is 7.2% of average load 0.536444 LDB: Average compute 0.005531 is 1.0% of average load 0.536444 LDB: Partitioning computes with target load 0.053644 LDB: Increased migratable compute count from 513 to 513 LDB: Largest unpartitionable compute is 0.015653 LDB: ============== END OF LOAD BALANCING =============== 1.19149 LDB: =============== DONE WITH MIGRATION ================ 1.19999 Info: Initial time: 8 CPUs 0.00827798 s/step 0.047905 days/ns 7.28886 MB memory LDB: ============= START OF LOAD BALANCING ============== 1.36911 LDB: ============== END OF LOAD BALANCING =============== 1.36966 LDB: =============== DONE WITH MIGRATION ================ 1.37157 LDB: ============= START OF LOAD BALANCING ============== 2.04026 LDB: Largest compute 18 load 0.041898 is 7.8% of average load 0.539234 LDB: Average compute 0.005561 is 1.0% of average load 0.539234 LDB: TIME 2.0416 LOAD: AVG 0.539234 MAX 0.624541 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 None MEM: 7.3532 MB LDB: TIME 2.04213 LOAD: AVG 0.539234 MAX 0.542324 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 TorusLB MEM: 7.377 MB LDB: ============== END OF LOAD BALANCING =============== 2.04543 LDB: =============== DONE WITH MIGRATION ================ 2.05221 Info: Initial time: 8 CPUs 0.00836348 s/step 0.0483998 days/ns 7.31621 MB memory LDB: ============= START OF LOAD BALANCING ============== 2.86832 LDB: Largest compute 21 load 0.051863 is 7.5% of average load 0.690388 LDB: Average compute 0.007192 is 1.0% of average load 0.690388 LDB: TIME 2.86967 LOAD: AVG 0.690388 MAX 0.701857 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 None MEM: 7.39986 MB LDB: TIME 2.86979 LOAD: AVG 0.690388 MAX 0.701857 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 RefineTorusLB MEM: 7.41545 MB LDB: TIME 2.86983 LOAD: AVG 0.690388 MAX 0.701857 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 RefineTorusLB MEM: 7.41545 MB LDB: ============== END OF LOAD BALANCING =============== 2.87173 LDB: =============== DONE WITH MIGRATION ================ 2.87883 Info: Initial time: 8 CPUs 0.00816636 s/step 0.047259 days/ns 7.37926 MB memory LDB: ============= START OF LOAD BALANCING ============== 3.68867 LDB: Largest compute 18 load 0.052058 is 7.5% of average load 0.692521 LDB: Average compute 0.007202 is 1.0% of average load 0.692521 LDB: TIME 3.69001 LOAD: AVG 0.692521 MAX 0.709778 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 None MEM: 7.47679 MB LDB: TIME 3.69014 LOAD: AVG 0.692521 MAX 0.709778 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 RefineTorusLB MEM: 7.49239 MB LDB: TIME 3.69018 LOAD: AVG 0.692521 MAX 0.709778 PROXIES: TOTAL 95 MAXPE 14 MAXPATCH 5 RefineTorusLB MEM: 7.49239 MB LDB: ============== END OF LOAD BALANCING =============== 3.69211 LDB: =============== DONE WITH MIGRATION ================ 3.69927 ADAPTEMP: STEP 9710400 TEMP 464.25 ENERGY -16054.86986 ENERGYAVG -1272.788413 ENERGYVAR 642.8887221 Info: Benchmark time: 8 CPUs 0.008106169701 s/step 0.04691070429 days/ns 7.516311646 MB memory ENERGY: 9710400 68.0445 134.4528 157.8569 0.0000 -18822.2698 2398.5997 0.0000 0.0000 3953.9623 -12109.3536 357.8963 -16063.3159 -12100.0320 339.2058 709.4781 814.6047 57571.0313 283.6217 282.9615 OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE AT STEP 9710400 The last position output (seq=9710400) takes 0.004 seconds, 7.504 MB of memory in use Info: Benchmark time: 8 CPUs 0.008065099716 s/step 0.04667303076 days/ns 7.632339478 MB memory Info: Benchmark time: 8 CPUs 0.008059279919 s/step 0.04663935138 days/ns 7.609725952 MB memory ADAPTEMP: STEP 9710800 TEMP 489.4245125 ENERGY -15647.64429 ENERGYAVG -4124.77696 ENERGYVAR 203393.7836 ENERGY: 9710800 72.9306 127.2635 159.2131 0.0000 -18259.8661 2248.4027 0.0000 0.0000 4214.6105 -11437.4456 381.4891 -15652.0561 -11425.5505 366.8049 483.1132 585.8493 57571.0313 581.8964 581.9164 WRITING COORDINATES TO DCD FILE AT STEP 9710800 The last position output (seq=9710800) takes 0.001 seconds, 7.645 MB of memory in use ADAPTEMP: STEP 9711200 TEMP 596.4666786 ENERGY -15060.59196 ENERGYAVG -3342.92527 ENERGYVAR 727.7179289 WRITING COORDINATES TO DCD FILE AT STEP 9711200 The last position output (seq=9711200) takes 0.001 seconds, 7.660 MB of memory in use ENERGY: 9711200 79.7409 151.0697 155.2528 0.0000 -17635.1196 2182.2684 0.0000 0.0000 4638.7770 -10428.0109 419.8829 -15066.7879 -10417.4705 395.6689 1248.3191 1362.2988 57571.0313 1169.6523 1170.0051 ADAPTEMP: STEP 9711600 TEMP 574.3613746 ENERGY -14419.23408 ENERGYAVG -6413.2182 ENERGYVAR 426.2572188 ENERGY: 9711600 101.6429 176.5734 153.1257 0.0000 -17103.3778 2260.1324 0.0000 0.0000 5025.8527 -9386.0506 454.9194 -14411.9034 -9376.5751 441.4470 2886.1615 2990.4158 57571.0313 2196.9698 2196.8669 WRITING COORDINATES TO DCD FILE AT STEP 9711600 The last position output (seq=9711600) takes 0.001 seconds, 7.683 MB of memory in use ADAPTEMP: STEP 9712000 TEMP 320.1016491 ENERGY -14879.31995 ENERGYAVG -1306.092796 ENERGYVAR 1380.910461 TIMING: 9712000 CPU: 16.481, 0.00818051/step Wall: 16.4857, 0.00818246/step, 1136.45 hours remaining, 7.751450 MB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 9712000 64.0824 159.8516 152.2772 0.0000 -17312.6438 2056.4717 0.0000 0.0000 4778.3249 -10101.6361 432.5142 -14879.9610 -10087.3393 448.0220 1420.6683 1540.8587 57571.0313 1960.9623 1961.1321 WRITING COORDINATES TO DCD FILE AT STEP 9712000 The last position output (seq=9712000) takes 0.001 seconds, 7.773 MB of memory in use ADAPTEMP: STEP 9712400 TEMP 315.6010941 ENERGY -15085.35818 ENERGYAVG -2869.695372 ENERGYVAR 295.7888367 ENERGY: 9712400 69.8667 132.7724 140.5644 0.0000 -17627.4870 2161.4695 0.0000 0.0000 4412.8112 -10710.0029 399.4294 -15122.8141 -10699.0176 413.9537 1024.3393 1131.6736 57571.0313 1423.5254 1423.4716 WRITING COORDINATES TO DCD FILE AT STEP 9712400 The last position output (seq=9712400) takes 0.001 seconds, 7.763 MB of memory in use ADAPTEMP: STEP 9712800 TEMP 296.5571353 ENERGY -15607.0641 ENERGYAVG -3827.210426 ENERGYVAR 101.8297852 ENERGY: 9712800 57.3855 139.0176 136.7853 0.0000 -18094.8445 2167.7932 0.0000 0.0000 4121.9984 -11471.8646 373.1062 -15593.8629 -11462.9668 388.2359 539.3500 641.6920 57571.0313 1214.1742 1213.8197 WRITING COORDINATES TO DCD FILE AT STEP 9712800 The last position output (seq=9712800) takes 0.001 seconds, 7.749 MB of memory in use ADAPTEMP: STEP 9713200 TEMP 293.9958901 ENERGY -15914.17185 ENERGYAVG -12923.58366 ENERGYVAR 41401.01413 ENERGY: 9713200 53.7929 123.7112 138.8440 0.0000 -18378.6182 2142.8639 0.0000 0.0000 3847.0596 -12072.3466 348.2199 -15919.4062 -12060.8383 360.1529 -169.5992 -67.5015 57571.0313 364.7112 364.5646 WRITING COORDINATES TO DCD FILE AT STEP 9713200 The last position output (seq=9713200) takes 0.002 seconds, 7.723 MB of memory in use ADAPTEMP: STEP 9713600 TEMP 294.182207 ENERGY -16129.12753 ENERGYAVG -13081.80199 ENERGYVAR 43509.49584 TIMING: 9713600 CPU: 29.6299, 0.00821801/step Wall: 29.6362, 0.00821908/step, 1141.53 hours remaining, 7.751358 MB of memory in use. ENERGY: 9713600 59.3629 128.3236 153.2208 0.0000 -18790.5519 2313.7456 0.0000 0.0000 3671.6609 -12464.2381 332.3435 -16135.8990 -12455.5254 345.1153 -72.4279 14.3641 57571.0313 26.0927 26.0757 WRITING COORDINATES TO DCD FILE AT STEP 9713600 The last position output (seq=9713600) takes 0.001 seconds, 7.739 MB of memory in use