Charm++> Running on MPI version: 1.2 multi-thread support: 0/0 Charm++> MPI timer is synchronized! 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 50914 for mpi-linux-amd64-mpt-iccstatic Info: Built Wed Aug 6 01:10:03 CEST 2008 by rtarek on service2 Info: 1 NAMD 2.6 Linux-amd64 1 r2i3n14 amara Info: Running on 1 processors. Info: 13837 kB of memory in use. Info: Memory usage based on mallinfo Info: Configuration file is test_const.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE EQUIL_HPO4_wat.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 10 Info: PERIODIC CELL BASIS 1 71.3174 0 0 Info: PERIODIC CELL BASIS 2 0 70.9395 0 Info: PERIODIC CELL BASIS 3 0 0 71.034 Info: PERIODIC CELL CENTER -0.12 0.24 -0.24 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB Info: LDB PERIOD 2000 steps Info: FIRST LDB TIMESTEP 50 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: MAX SELF PARTITIONS 20 Info: MAX PAIR PARTITIONS 8 Info: SELF PARTITION ATOMS 154 Info: SELF2 PARTITION ATOMS 0 Info: PAIR PARTITION ATOMS 318 Info: PAIR2 PARTITION ATOMS 637 Info: MIN ATOMS PER PATCH 100 Info: VELOCITY FILE EQUIL_HPO4_wat.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 test_const.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME test_const.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME test_const Info: RESTART FILENAME test_const.restart Info: RESTART FREQUENCY 50 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 15 Info: SWITCHING OFF 16 Info: PAIRLIST DISTANCE 18 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 0.615 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 21.115 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 295 Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE Info: TARGET PRESSURE IS 1.01325 BAR Info: OSCILLATION PERIOD IS 200 FS Info: DECAY TIME IS 100 FS Info: PISTON TEMPERATURE IS 295 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS -0.000917947 -0.000917947 -0.000917947 Info: CELL FLUCTUATION IS ISOTROPIC Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-06 Info: PME EWALD COEFFICIENT 0.190674 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 75 75 75 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 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 1259226213 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB EQUIL_HPO4_wat.coor Info: STRUCTURE FILE overlay.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_satpati_gdp_hpo4.prm Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 261 BONDS Info: 663 ANGLES Info: 1131 DIHEDRAL Info: 70 IMPROPER Info: 6 CROSSTERM Info: 162 VDW Info: 0 VDW_PAIRS Warning: Ignored 13135 bonds with zero force constants. Warning: Will get H-H distance in rigid H2O from H-O-H angle. Info: **************************** Info: STRUCTURE SUMMARY: Info: 39412 ATOMS Info: 26275 BONDS Info: 13142 ANGLES Info: 3 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 39406 RIGID BONDS Info: 78830 DEGREES OF FREEDOM Info: 13141 HYDROGEN GROUPS Info: TOTAL MASS = 236753 amu Info: TOTAL CHARGE = 8.9407e-08 e Info: ***************************** Info: Entering startup phase 0 with 24959 kB of memory in use. Info: Entering startup phase 1 with 24959 kB of memory in use. Info: Entering startup phase 2 with 29748 kB of memory in use. Info: Entering startup phase 3 with 30056 kB 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 -0.000197914 -0.0206557 0.0186922 Info: LARGEST PATCH (15) HAS 1491 ATOMS Info: CREATING 2679 COMPUTE OBJECTS Info: Entering startup phase 4 with 35181 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 36858 kB of memory in use. Info: Entering startup phase 6 with 36857 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 36859 kB of memory in use. Info: CREATING 2679 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 833 POINTS Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.54074e-33 AT 21.9986 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 2.06776e-20 AT 21.9986 Info: Entering startup phase 8 with 40902 kB of memory in use. Info: Finished startup with 44518 kB of memory in use. TCL: Running for 50010 steps ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 3.2624 13.2535 0.1623 0.0000 -168214.1163 20534.9956 0.0000 0.0000 14832.4298 -132830.0127 189.3700 -132785.3622 -132785.3622 189.3700 1371.7886 1385.9375 359376.6830 1371.7886 1385.9375 OPENING EXTENDED SYSTEM TRAJECTORY FILE Info: Initial time: 1 CPUs 1.44411 s/step 8.35709 days/ns 214015 kB memory WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 50 WRITING COORDINATES TO RESTART FILE AT STEP 50 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 50 FINISHED WRITING RESTART VELOCITIES Info: Initial time: 1 CPUs 1.4191 s/step 8.21236 days/ns 218219 kB memory ENERGY: 100 4.4569 15.2976 0.2787 0.0000 -161954.3782 17619.4631 0.0000 0.0000 18503.0191 -125811.8627 236.2335 -125777.3734 -125785.2884 222.4745 2.4223 10.5637 369331.2335 329.7422 329.1157 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 1.39949 s/step 8.09887 days/ns 219745 kB memory WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 150 WRITING COORDINATES TO RESTART FILE AT STEP 150 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 150 FINISHED WRITING RESTART VELOCITIES