Info: NAMD 2.5 for HPUX 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 050612 for net-hp-acc Info: Built Fri Sep 26 17:42:53 CDT 2003 by jim on ganymede.ks.uiuc.edu Info: Sending usage information to NAMD developers via UDP. Sent data is: Info: 1 NAMD 2.5 HPUX 8 crick eheneber Info: Running on 8 processors. Info: 1472 kB of memory in use. Measuring processor speeds... Done. Info: Configuration file is gcn4_5h_eq.conf TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 10 Info: PERIODIC CELL BASIS 1 69.12 0 0 Info: PERIODIC CELL BASIS 2 0 66.78 0 Info: PERIODIC CELL BASIS 3 0 0 60.77 Info: PERIODIC CELL CENTER 19.95 17.2 7.96 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. 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: 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: INITIAL TEMPERATURE 298 Info: CENTER OF MASS MOVING? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME gcn4_5H_eq.dcd Info: DCD FREQUENCY 500 Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE Info: XST FILENAME gcn4_5H_eq.xst Info: XST FREQUENCY 500 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME gcn4_5H_eq Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME gcn4_5H_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: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 298 Info: LANGEVIN DAMPING COEFFICIENT IS 5 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 52 52 52 Info: Attempting to read FFTW data from FFTW_NAMD_2.5_HPUX.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.5_HPUX.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 1103662102 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ionized.pdb Info: STRUCTURE FILE ionized.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS ../common/par_all27_prot_lipid.inp Info: SUMMARY OF PARAMETERS: Info: 179 BONDS Info: 441 ANGLES Info: 534 DIHEDRAL Info: 49 IMPROPER Info: 89 VDW Info: 0 VDW_PAIRS FATAL ERROR: Asymmetric water molecule found??? This can't be right.