 |
 |
 |
 |
 |
 |
||
 |
 |
 |
 |
 |
| 4 | 1/1 | 返回列表 |
| 查看: 1030 | 回復(fù): 3 | ||
[求助]
NAMD tutorial出錯
|
|
ubq_ws_eq.log里的內(nèi)容如下，提示錯誤的地方用紅色標(biāo)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運行所需的pdb，psf，conf及所需的力場文件都放在C:\Users\Administrator目錄下，NAMD解壓在D:\Program Files\University of Illinois\VMD目錄下，設(shè)置了環(huán)境變量，CMD在C:\Users\Administrator下輸入的命令。conf文件是從namd-tutorial-files中考出來的，未作改動。求高手指教啊，本人剛接觸NAMD，還請大家包涵。 [ Last edited by qbin1304 on 2013-1-9 at 17:21 ] |
回復(fù)此樓» 猜你喜歡
0856，材料與化工321分求調(diào)劑
已經(jīng)有6人回復(fù)
-
0703化學(xué)求調(diào)劑，各位老師看看我�。�！
已經(jīng)有5人回復(fù)
-
266分，求材料冶金能源化工等調(diào)劑
已經(jīng)有7人回復(fù)
-
張芳銘-中國農(nóng)業(yè)大學(xué)-環(huán)境工程專碩-298
已經(jīng)有3人回復(fù)
-
070300化學(xué)求調(diào)劑
已經(jīng)有4人回復(fù)
-
086000調(diào)劑
已經(jīng)有3人回復(fù)
-
320分，材料與化工專業(yè)，求調(diào)劑
已經(jīng)有4人回復(fù)
-
265求調(diào)劑
已經(jīng)有7人回復(fù)
-
295材料工程專碩求調(diào)劑
已經(jīng)有4人回復(fù)
-
高溫高壓反應(yīng)求助
已經(jīng)有4人回復(fù)
» 本主題相關(guān)價值貼推薦，對您同樣有幫助:
- 【求助】做NAMD的1K4C.pdb時候出現(xiàn)的錯誤
已經(jīng)有30人回復(fù)
- 【求助】各位好：我按照NAMD tutorial做出來的RMSD圖沒有tutorial漂亮
已經(jīng)有6人回復(fù)
- 【求助】namd 出錯Periodic cell has become too small for original patch grid!
已經(jīng)有10人回復(fù)
- 【求助】namd tutorial遇到問題
已經(jīng)有10人回復(fù)
2樓2013-01-09 20:59:16
3樓2015-04-27 10:03:18
gn02530640
銀蟲 (小有名氣)
- 應(yīng)助: 8 (幼兒園)
- 金幣: 314.5
- 紅花: 1
- 帖子: 139
- 在線: 86.6小時
- 蟲號: 2796302
- 注冊: 2013-11-12
- 性別: GG
- 專業(yè): 理論和計算化學(xué)
4樓2015-04-27 12:38:47
相關(guān)版塊跳轉(zhuǎn)
我要訂閱樓主 qbin1304 的主題更新
| 4 | 1/1 | 返回列表 |
| 最具人氣熱帖推薦 [查看全部] | 作者 | 回/看 | 最后發(fā)表 | |
|---|---|---|---|---|
|
[考研] 學(xué)碩274求調(diào)劑 +5 | Li李魚 2026-03-26 | 5/250 |
|
|---|---|---|---|---|
|
[考研] 322求調(diào)劑 +3 | 宋明欣 2026-03-27 | 3/150 |
|
|
|
[考研] 307求調(diào)劑 +8 | 超級伊昂大王 2026-03-24 | 9/450 |
|
|
|
[考研] 303求調(diào)劑 +7 | 安憶靈 2026-03-22 | 8/400 |
|
|
|
[考研] 求調(diào)劑 +3 | 劉柯@ 2026-03-24 | 4/200 |
|
|
|
[考研] 材料求調(diào)劑 +8 | @taotao 2026-03-21 | 8/400 |
|
|
|
[考研] 0703化學(xué)338求調(diào)劑！ +6 | Zuhui0306 2026-03-26 | 7/350 |
|
|
|
[碩博家園] 北京林業(yè)大學(xué)碩導(dǎo)招生廣告 +6 | kongweilin 2026-03-26 | 8/400 |
|
|
|
[考研] 336材料求調(diào)劑 +7 | 陳瀅瑩 2026-03-26 | 9/450 |
|
|
|
[考研] 325求調(diào)劑 +3 | Aoyijiang 2026-03-23 | 3/150 |
|
|
|
[考研] 材料277求調(diào)劑 +5 | min3 2026-03-24 | 5/250 |
|
|
|
[考研] 調(diào)劑310 +3 | 溫柔的晚安 2026-03-25 | 4/200 |
|
|
|
[考研] 334分 一志愿武理-080500 材料求調(diào)劑 +4 | 李李不服輸 2026-03-25 | 4/200 |
|
|
|
[考研] 340求調(diào)劑 +5 | 話梅糖111 2026-03-24 | 5/250 |
|
|
|
[考研] 求調(diào)劑 +7 | 十三加油 2026-03-21 | 7/350 |
|
|
|
[考研] 341求調(diào)劑(一志愿湖南大學(xué)070300) +5 | 番茄頭--- 2026-03-22 | 6/300 |
|
|
|
[考研] 070300，一志愿北航320求調(diào)劑 +3 | Jerry0216 2026-03-22 | 5/250 |
|
|
|
[考研] 280分求調(diào)劑 一志愿085802 +4 | PUMPT 2026-03-22 | 7/350 |
|
|
|
[考研] 308求調(diào)劑 +3 | 墨墨漠 2026-03-21 | 3/150 |
|
|
|
[考研] 一志愿深大，0703化學(xué)，總分302，求調(diào)劑 +4 | 七月-七七 2026-03-21 | 4/200 |
|