Charm++: standalone mode (not using charmrun) Info: NAMD 2.6b1 for Win32-i686 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 Kale et al., J. Comp. Phys. 151:283-312 (1999) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 50900 for net-win32-smp Info: Built Fri Jul 29 12:33:47 2005 by administrator on malta Info: Running on 1 processors. Info: 0 kB of memory in use. Info: Configuration file is Consensus_ws_eq.conf TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 10 Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 2000 steps Info: FIRST LDB TIMESTEP 50 Info: LDB BACKGROUND SCALING 1 Info: HOM 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: INITIAL TEMPERATURE 310 Info: CENTER OF MASS MOVING? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME Consensus_autopsf_ws_eq.dcd Info: DCD FREQUENCY 250 Info: DCD FIRST STEP 250 Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME Consensus_autopsf_ws_eq Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME Consensus_autopsf_ws_eq.restart Info: RESTART FREQUENCY 500 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 Info: PAIRLIST DISTANCE 13.5 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 16 Info: ENERGY OUTPUT STEPS 100 Info: PRESSURE OUTPUT STEPS 100 Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE Info: RADIUS #1 26 Info: FORCE CONSTANT #1 10 Info: EXPONENT #1 2 Info: SPHERE BOUNDARY CENTER(12.4316, -2.22414, 15.281) Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Info: VELOCITY REASSIGNMENT FREQ 5 Info: VELOCITY REASSIGNMENT TEMP 0 Info: VELOCITY REASSIGNMENT INCR 1 Info: VELOCITY REASSIGNMENT HOLD 310 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-008 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1392711435 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ../common/Consensus_autopsf_ws.pdb Info: STRUCTURE FILE ../common/Consensus_autopsf_ws.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS ../common/par_all27_prot_lipid.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 179 BONDS Info: 441 ANGLES Info: 534 DIHEDRAL Info: 49 IMPROPER Info: 89 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 140190 ATOMS Info: 95945 BONDS Info: 57545 ANGLES Info: 19350 DIHEDRALS Info: 1153 IMPROPERS Info: 0 EXCLUSIONS Info: 136591 RIGID BONDS Info: 283979 DEGREES OF FREEDOM Info: 47924 HYDROGEN GROUPS Info: TOTAL MASS = 849748 amu Info: TOTAL CHARGE = 2 e Info: ***************************** BRACKET: 2.38382e-007 133866 -2.24072e+012 -2.23352e+012 -2.23705e+012 Warning: Bad global exclusion count, possible error! Warning: Increasing cutoff during minimization may avoid this. PRESSURE: 200 0 0 0 0 0 0 0 0 0 GPRESSURE: 200 0 0 0 0 0 0 0 0 0 Info: Benchmark time: 1 CPUs 4.65438 s/step 53.8701 days/ns 0 kB memory ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG ENERGY: 200 465001.6796 50117.3438 2378.4312 1962.0622 -507316.7550 1944377.6461 99999999.9999 0.0000 0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000 REINITIALIZING VELOCITIES AT STEP 200 TO 310 KELVIN. TCL: Running for 500000 steps REASSIGNING VELOCITIES AT STEP 200 TO 40 KELVIN. ERROR: Constraint failure in RATTLE algorithm for atom 6790! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4469! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 308! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4377! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4463! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4790! ERROR: Constraint failure; simulation has become unstable. ERROR: Exiting prematurely. ========================================== WallClock: 941.328003 CPUTime: 941.328003 Memory: 0 kB Program finished.