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qbin1304专家顾问
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[求助]
NAMD tutorial出错
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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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