Charm++: standalone mode (not using charmrun) Info: NAMD 2.5b1 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: Running on 1 processors. Info: 0 kB of memory in use. Measuring processor speeds... Done. Info: Configuration file is autoimd.namd TCL: AUTOIMD HOST: dionizos PID: 1680 TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 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: 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 310 Info: CENTER OF MASS MOVING? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: NO DCD TRAJECTORY OUTPUT Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME autoimd_out Info: BINARY OUTPUT FILES WILL BE USED Info: NO RESTART FILE Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 Info: PAIRLIST DISTANCE 14 Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.5 Info: TIMING OUTPUT STEPS 1000 Info: FIXED ATOMS ACTIVE Info: INTERACTIVE MD ACTIVE Info: INTERACTIVE MD PORT 6075 Info: INTERACTIVE MD FREQ 2 Info: WILL AWAIT INTERACTIVE MD CONNECTION Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN DAMPING COEFFICIENT IS 3 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS 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-005 Info: MAX ITERATIONS : 100 Info: RANDOM NUMBER SEED 1118845302 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB autoimd.pdb Info: STRUCTURE FILE autoimd.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS alanin.params abnormal program termination