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tangjikede

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专业: 固体力学

thanks

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41楼2009-08-05 21:48:50

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tangjikede

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注册: 2006-10-22
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专业: 固体力学

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我刚下载了一个VMD187，安装了后怎么点击后，闪了一下一个黑框就没了，是电脑系统的原因吗

[ Last edited by tangjikede on 2009-8-7 at 11:31 ]

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42楼2009-08-05 21:51:15

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anquren

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运行NAMD出现如下错误,原因是什么?
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 NAMD  2.6  Linux-i686  1
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: TIMESTEP             1
Info: NUMBER OF STEPS       0
Info: STEPS PER CYCLE       20
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD          4000 steps
Info: FIRST LDB TIMESTEP    100
Info: LDB BACKGROUND SCALING 1
Info: HOM 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: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 298
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC          1
Info: EXCLUDE             SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR    1
Info: DCD FILENAME          rgbinw.dcd
Info: DCD FREQUENCY       50
Info: DCD FIRST STEP       50
Info: XST FILENAME          rgbinw.xst
Info: XST FREQUENCY       50
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME       rgbinw
Info: RESTART FILENAME    rgbinw.restart
Info: RESTART FREQUENCY    1000
Info: SWITCHING ACTIVE
Info: SWITCHING ON          9
Info: SWITCHING OFF       10
Info: PAIRLIST DISTANCE    12
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       14.5
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
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 SEED    1249824237
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB       rgbinro1aw.pdb
Info: STRUCTURE FILE       rgbinro1aw.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS          par_all27_prot_lipid_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
USING VALUES  k=130  theta0=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 C  NH1  CT1  C  NH1  CT1  C  NH1
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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43楼2009-08-11 11:50:27

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