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qbin1304

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专业: 化学生物学与生物有机化学

[求助] NAMD tutorial出错

ubq_ws_eq.log里的内容如下，提示错误的地方用红色标出了
Charm++: standalone mode (not using charmrun)
Charm++ warning> fences and atomic operations not available in native assembly
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
[0] isomalloc.c> Disabling isomalloc because mmap() does not work
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.017 seconds.
Info: NAMD 2.9 for Win32-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60400 for multicore-win32
Info: Built Mon Apr 30 14:10:39 CDT 2012 by jcphill on honor
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0190001 s
Info: 3.05469 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is ubq_ws_eq.conf
Info: Working in the current directory C:\Users\Administrator
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP             2
Info: NUMBER OF STEPS       0
Info: STEPS PER CYCLE       10
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
Info: LDB PERIOD          2000 steps
Info: FIRST LDB TIMESTEP    50
Info: LAST LDB TIMESTEP    -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC          1
Info: EXCLUDE             SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME          ubq_ws_eq.dcd
Info: DCD FREQUENCY       250
Info: DCD FIRST STEP       250
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME       ubq_ws_eq
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME    ubq_ws_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    14
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       16.5
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS  100
Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE
Info: RADIUS #1             26
Info: FORCE CONSTANT #1    10
Info: EXPONENT #1          2
Info: SPHERE BOUNDARY CENTER(30.3082, 28.805, 15.354)
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 1 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-008
Info:       MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED    1357633068
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB       ../common/ubq_ws.pdb
Info: STRUCTURE FILE       ../common/ubq_ws.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS          ../common/par_all27_prot_lipid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: UNABLE TO OPEN CHARMM PARAMETER FILE ../common/par_all27_prot_lipid.inp
NAMD运行所需的pdb，psf，conf及所需的力场文件都放在C:\Users\Administrator目录下，NAMD解压在D:\Program Files\University of Illinois\VMD目录下，设置了环境变量，CMD在C:\Users\Administrator下输入的命令。conf文件是从namd-tutorial-files中考出来的，未作改动。求高手指教啊，本人刚接触NAMD，还请大家包涵。

[ Last edited by qbin1304 on 2013-1-9 at 17:21 ]

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