Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 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 Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-iccstatic
Info: Built Wed Aug 30 12:54:30 CDT 2006 by jim on kyoto.ks.uiuc.edu
Info: 1 NAMD2.6Linux-i6861
Info: Running on 1 processors.
Info: 7240 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is rgbiw.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP1
Info: NUMBER OF STEPS0
Info: STEPS PER CYCLE20
Info: LOAD BALANCE STRATEGYOther
Info: LDB PERIOD4000 steps
Info: FIRST LDB TIMESTEP100
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS50
Info: MAX PAIR PARTITIONS20
Info: SELF PARTITION ATOMS125
Info: PAIR PARTITION ATOMS200
Info: PAIR2 PARTITION ATOMS400
Info: MIN ATOMS PER PATCH100
Info: INITIAL TEMPERATURE298
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC1
Info: EXCLUDESCALED ONE-FOUR
Info: 1-4 SCALE FACTOR1
Info: DCD FILENAMErgbinw.dcd
Info: DCD FREQUENCY50
Info: DCD FIRST STEP50
Info: XST FILENAMErgbinw.xst
Info: XST FREQUENCY50
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAMErgbinw
Info: RESTART FILENAMErgbinw.restart
Info: RESTART FREQUENCY1000
Info: SWITCHING ACTIVE
Info: SWITCHING ON9
Info: SWITCHING OFF10
Info: PAIRLIST DISTANCE12
Info: PAIRLIST SHRINK RATE0.01
Info: PAIRLIST GROW RATE0.01
Info: PAIRLIST TRIGGER0.3
Info: PAIRLISTS PER CYCLE2
Info: PAIRLISTS ENABLED
Info: MARGIN0
Info: HYDROGEN GROUP CUTOFF2.5
Info: PATCH DIMENSION14.5
Info: ENERGY OUTPUT STEPS100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS1000
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED1249824237
Info: USE HYDROGEN BONDS?NO
Info: COORDINATE PDBrgbinro1aw.pdb
Info: STRUCTURE FILErgbinro1aw.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERSpar_all27_prot_lipid_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUESk=130theta0=107.5 k_ub=0 r_ub=0
USING VALUESk=130theta0=107 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 299 BONDS
Info: 729 ANGLES
Info: 1145 DIHEDRAL
Info: 84 IMPROPER
Info: 0 CROSSTERM
Info: 161 VDW
Info: 0 VDW_PAIRS
FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CNH1CT1CNH1CT1CNH1
Stack Traceback:
[0] _ZN10Parameters22assign_crossterm_indexEPcS0_S0_S0_S0_S0_S0_S0_P9crossterm+0x34b[0x828a447]
[1] _ZN8Molecule15read_crosstermsEP8_IO_FILEP10Parameters+0x29f[0x8265027]
[2] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x1129[0x8262fed]
[3] _ZN8MoleculeC9EP13SimParametersP10ParametersPc+0x246[0x8261e02]
[4] _ZN8MoleculeC1EP13SimParametersP10ParametersPc+0x14[0x82665d0]
[5] _ZN9NamdState14configListInitEP10ConfigList+0x49b[0x827abc7]
[6] _ZN9ScriptTcl9initcheckEv+0x5e[0x82b9f8e]
[7] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e[0x82b74a2]
[8] TclInvokeStringCommand+0x7f[0x8395d58]
[9] namd2 [0x83ca7c1]
[10] Tcl_EvalEx+0x1c3[0x83cae4e]
[11] Tcl_EvalFile+0x138[0x83c2afa]
[12] _ZN9ScriptTcl3runEPc+0x1a[0x82b6a86]
[13] main+0x1d6[0x80df19a]
[14] __libc_start_main+0xbc[0x4012dbac]
[15] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x59[0x80dba71]
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