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.