Charm++: standalone mode (not using charmrun) Info: NAMD 2.5b1 for Linux-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: Sending usage information to NAMD developers via UDP. Info: Sent data is: 1 NAMD 2.5b1 Linux-i686 1 thinktank cheri Info: Running on 1 processors. Info: 4301 kB of memory in use. Measuring processor speeds... Done. Info: Configuration file is Simulated_annealing TCL: Suspending until startup complete. Warning: The parameter fullElectFrequency now defaults to nonbondedFreq (1) rather than stepsPerCycle. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 100 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 77.777 0 0 Info: PERIODIC CELL BASIS 2 0 73.172 0 Info: PERIODIC CELL BASIS 3 0 0 75.527 Info: PERIODIC CELL CENTER -7.41817 -19.5895 -30.381 Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 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 0 Info: CENTER OF MASS MOVING? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME output/W1A1_sim.dcd Info: DCD FREQUENCY 1000 Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE Info: XST FILENAME output/W1A1_sim.xst Info: XST FREQUENCY 10 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME output/W1A1_sim Info: NO RESTART FILE Info: SWITCHING ACTIVE Info: SWITCHING ON 8 Info: SWITCHING OFF 10 Info: PAIRLIST DISTANCE 13.5 Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16 Info: ENERGY OUTPUT STEPS 100 Info: INTERACTIVE MD ACTIVE Info: INTERACTIVE MD PORT 1 Info: INTERACTIVE MD FREQ 10 Info: CONJUGATE GRADIENT MINIMIZATION ACTIVE Info: LINE MINIMIZATION GOAL = 0.0001 Info: BABY STEP SIZE = 0.01 Info: TINY STEP SIZE = 1e-06 Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-06 Info: PME EWALD COEFFICIENT 0.312341 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 80 80 80 Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1 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-05 Info: MAX ITERATIONS : 100 Info: RANDOM NUMBER SEED 1063663498 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB output/W1A1_wb.pdb Info: STRUCTURE FILE output/W1A1_wb.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all22_prot.inp Warning: DUPLICATE DIHEDRAL ENTRY FOR CP1-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CP3-N-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-NH1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 1 k=0.2 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.27 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 2 k=0.2 n=1 delta=0 k=0.27 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-NH1-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-NH1-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-NH1-C-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-SM-SM-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=4.1 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-SM-SM-CT2 PREVIOUS VALUES MULTIPLICITY: 2 k=1 n=1 delta=0 k=4.1 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.9 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 1 k=0.2 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.27 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-CPH1-CPH1 PREVIOUS VALUES MULTIPLICITY: 2 k=0.2 n=1 delta=0 k=0.27 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-S-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.37 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-NH1-C-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-NH1-C-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.6 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=2.5 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-S-CT2-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.37 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-SM-SM-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=4.1 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-SM-SM-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=1 n=1 delta=0 k=4.1 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.9 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.33 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.18 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT1 PREVIOUS VALUES MULTIPLICITY: 2 k=1.33 n=1 delta=0 k=0.18 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.32 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.33 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.18 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=1.33 n=1 delta=0 k=0.18 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.32 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=1.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.3 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 2 k=1.3 n=1 delta=0 k=0.3 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.42 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=1.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.3 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT2 PREVIOUS VALUES MULTIPLICITY: 2 k=1.3 n=1 delta=0 k=0.3 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.42 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=1.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.3 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=1.3 n=1 delta=0 k=0.3 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.42 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.15 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT1 PREVIOUS VALUES MULTIPLICITY: 2 k=0.24 n=1 delta=0 k=0.15 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.27 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=0.24 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.15 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT3 PREVIOUS VALUES MULTIPLICITY: 2 k=0.24 n=1 delta=0 k=0.15 n=2 delta=0 INCREASING MULTIPLICITY TO: 3 k=0.27 n=3 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-N PREVIOUS VALUES MULTIPLICITY: 1 k=0.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=-0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-N PREVIOUS VALUES MULTIPLICITY: 1 k=0.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=-0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-N PREVIOUS VALUES MULTIPLICITY: 1 k=0.3 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=-0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-N-CP1 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-N-CP3 PREVIOUS VALUES MULTIPLICITY: 1 k=2.75 n=2 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.3 n=4 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-CC-CP1-CP2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR O-CC-CP1-HB PREVIOUS VALUES MULTIPLICITY: 1 k=0.4 n=1 delta=0 INCREASING MULTIPLICITY TO: 2 k=0.6 n=2 delta=0 Warning: DUPLICATE DIHEDRAL ENTRY FOR OB-CD-OS-CT2 PREVIOUS VALUES MULTIPLICITY: 1 k=0.965 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=3.85 n=2 delta=180 Warning: DUPLICATE DIHEDRAL ENTRY FOR OB-CD-OS-CT3 PREVIOUS VALUES MULTIPLICITY: 1 k=0.965 n=1 delta=180 INCREASING MULTIPLICITY TO: 2 k=3.85 n=2 delta=180 Info: SUMMARY OF PARAMETERS: Info: 139 BONDS Info: 343 ANGLES Info: 443 DIHEDRAL Info: 43 IMPROPER Info: 60 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 39363 ATOMS Info: 28910 BONDS Info: 24659 ANGLES Info: 20716 DIHEDRALS Info: 1345 IMPROPERS Info: 0 EXCLUSIONS Info: 35507 RIGID BONDS Info: 82579 DEGREES OF FREEDOM Info: 14412 HYDROGEN GROUPS Info: TOTAL MASS = 244915 amu Info: TOTAL CHARGE = 0.840005 e Info: ***************************** Info: Entering startup phase 0 with 9413 kB of memory in use. Info: Entering startup phase 1 with 9413 kB of memory in use. Info: Entering startup phase 2 with 13709 kB of memory in use. Info: Entering startup phase 3 with 13709 kB of memory in use. Info: PATCH GRID IS 4 (PERIODIC) BY 4 (PERIODIC) BY 4 (PERIODIC) Info: REMOVING COM VELOCITY 0 0 0 Info: Entering startup phase 4 with 19869 kB of memory in use. Info: PME using 1 (max of 1 and 1) processors for FFT and reciprocal sum. Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Entering startup phase 5 with 23973 kB of memory in use. Info: Entering startup phase 6 with 23973 kB of memory in use. Info: Entering startup phase 7 with 23973 kB of memory in use. Info: COULOMB TABLE R-SQUARED SPACING: 0.0625 Info: COULOMB TABLE SIZE: 1605 POINTS Info: NONZERO IMPRECISION IN COULOMB TABLE: 6.62391e-25 2.12068e-23 Info: NONZERO IMPRECISION IN COULOMB TABLE: 8.27181e-25 2.64698e-23 Warning: Interactive MD failed to bind to port 1. Warning: Interactive MD listening on port 1025. Info: Entering startup phase 8 with 26437 kB of memory in use. Info: Finished startup with 34869 kB of memory in use. Warning: Not all atoms have unique coordinates. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 13373540.4319 99999999.9999 1986.8588 99999999.9999 -111162.1731 5796362.1421 0.0000 0.0000 0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999 429831.6119 99999999.9999 99999999.9999 INITIAL STEP: 1e-06 GRADIENT TOLERANCE: nan