Jfreda

鐵蟲 (小有名氣)

應(yīng)助: 0 (幼兒園)
金幣: 21.8
帖子: 91
在線: 31.5小時
蟲號: 870275

[交流] mdrun時出錯

mdrun -s aa.tpr -o aa.trr -c aa.gro &
出現(xiàn)了如下的提示錯誤：
step 11: Water molecule starting at atom 180665 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 13: Water molecule starting at atom 180665 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 31 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -3.1653622e+06
Maximum force    =  9.5183238e+05 on atom 180665
Norm of force    =  2.3416899e+03

下面是我的em.mdp文件
em.mdp

er spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
cpp                =  /lib/cpp
constraints       =  none
define             =  -DFLEX_SPC

; Parameters describing what to do, when to stop and what to save
integrator       = steep
dt                   = 0.002
emtol             = 1000.0
emstep             = 0.01
nsteps             = 3000

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist          = 10
ns_type          = grid
rlist             = 1.0
coulombtype       = pme
rcoulomb          = 1.0
rvdw             = 1.0
fourierspacing    =0.12
pme_order          =4
optimize_fft       =yes

freezegrps    =Protein UNK POP
freezedim       =Y Y Y Y Y Y Y Y Y
我也嘗試了改變em.mdp文件中的一些參數(shù)(只對一個參數(shù)做了修改)：
1.em.mdp文件中的freezegrps改為Protein UNK能量能很好地收斂，下面是它的顯示結(jié)果：
Steepest Descents:
Tolerance (Fmax) =  1.00000e+03
Number of steps =       3000

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 1678 steps
Potential Energy  = -4.2245720e+06
Maximum force    =  9.5952905e+02 on atom 9032
Norm of force    =  1.1612597e+01

2.em.mdp文件中的emstep改為0.00001（參照別人的回答), 結(jié)果顯示為：
Steepest Descents:
Tolerance (Fmax) =  1.00000e+03
Number of steps =       3000

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 32 steps
Potential Energy  = -3.0919205e+06
Maximum force    =  9.1417908e+02 on atom 122811
Norm of force    =  1.1197423e+02
這樣的結(jié)果應(yīng)該是有問題的吧，只跑了32步。

3.integrator改為md, 結(jié)果為：
Writing final coordinates.

Average load imbalance: 0.2 %
Part of the total run time spent waiting due to load imbalance: 0.1 %

      Parallel run - timing based on wallclock.

            NODE (s) Real (s)    (%)
   Time: 7515.940 7515.940 100.0
                     2h05:15
            (Mnbf/s) (GFlops) (ns/day)  (hour/ns)
Performance:    63.678    3.946    0.115 208.755

gcq#290: "Oh, There Goes Gravity" (Eminem)

請問一下，我應(yīng)該怎么做才是合理的？謝謝！

回復(fù)此樓

» 猜你喜歡

288求調(diào)劑，一志愿華南理工大學071005 已經(jīng)有5人回復(fù)
一志愿中國海洋大學，生物學，301分，求調(diào)劑已經(jīng)有5人回復(fù)
294求調(diào)劑材料與化工專碩已經(jīng)有12人回復(fù)
0856調(diào)劑，是學校就去已經(jīng)有5人回復(fù)
0817 化學工程 299分求調(diào)劑有科研經(jīng)歷有二區(qū)文章已經(jīng)有13人回復(fù)
梁成偉老師課題組歡迎你的加入已經(jīng)有11人回復(fù)
復(fù)試調(diào)劑已經(jīng)有6人回復(fù)
0703化學調(diào)劑，六級已過，有科研經(jīng)歷已經(jīng)有11人回復(fù)
321求調(diào)劑已經(jīng)有10人回復(fù)
東華理工大學化材專業(yè)26屆碩士博士申請已經(jīng)有8人回復(fù)

» 本主題相關(guān)價值貼推薦，對您同樣有幫助:

Gromacs中，mdrun出錯已經(jīng)有5人回復(fù)
在gromacs中運行mdrun命令時出錯已經(jīng)有10人回復(fù)
vsap 5.2 環(huán)境和編譯問題已經(jīng)有14人回復(fù)
Gromacs做steep之后做cg出錯已經(jīng)有5人回復(fù)
編譯vasp出錯已經(jīng)有11人回復(fù)
gromacs做全原子模擬時候，突然到MD這一步出錯已經(jīng)有6人回復(fù)
【求助】安裝vasp出錯 make: *** [fftmpi_map.o] 錯誤 1【已解決】已經(jīng)有6人回復(fù)
【求助】vasp安裝編譯錯誤，請大家?guī)兔聪履抢锍鲥e了。已經(jīng)有6人回復(fù)
【求助成功】Vasp 5.2.11編譯出錯已經(jīng)有10人回復(fù)
【求助】在編譯時出錯已經(jīng)有6人回復(fù)
【求助】PBE0 計算Si、Ge能帶結(jié)構(gòu) 已經(jīng)有9人回復(fù)

» 搶金幣啦！回帖就可以得到:

查看全部散金貼

1樓 2011-04-18 18:28:08

已閱回復(fù)此樓關(guān)注TA 給TA發(fā)消息送TA紅花 TA的回帖

Jfreda

鐵蟲 (小有名氣)

應(yīng)助: 0 (幼兒園)
金幣: 21.8
帖子: 91
在線: 31.5小時
蟲號: 870275

引用回帖:

Originally posted by jawang at 2011-04-18 18:42:24:
Steepest Descents converged to Fmax < 1000 in 32 steps
Potential Energy  = -3.0919205e+06
Maximum force    =  9.1417908e+02 on atom 122811
Norm of force    =  1.1197423e+02
這樣的結(jié)果應(yīng)該是 ...

好的，謝謝，但是我想問一下freegroup和define有什么區(qū)別嗎？我的目的是在優(yōu)化的過程中逐步放開限制。

贊一下

回復(fù)此樓

3樓2011-04-18 19:10:46

已閱回復(fù)此樓關(guān)注TA 給TA發(fā)消息送TA紅花 TA的回帖

查看全部 6 個回答

jawang

木蟲 (正式寫手)

應(yīng)助: 3 (幼兒園)
金幣: 3533.7
帖子: 376
在線: 214.7小時
蟲號: 838608

★ ★ ★ ★
小木蟲(金幣+0.5):給個紅包，謝謝回帖
Jfreda(金幣+5): 2011-04-18 19:08:54
zh1987hs(金幣+3): 謝謝 2011-04-18 21:33:02

Steepest Descents converged to Fmax < 1000 in 32 steps
Potential Energy  = -3.0919205e+06
Maximum force    =  9.1417908e+02 on atom 122811
Norm of force    =  1.1197423e+02
這樣的結(jié)果應(yīng)該是有問題的吧，只跑了32步。

雖然只跑了32步，不過你的力已經(jīng)基本收斂了，應(yīng)該沒有什么問題了。應(yīng)該不用freegroup,如果要限制原子的話，可以嘗試使用define.

贊一下(2人)

回復(fù)此樓

2樓2011-04-18 18:42:24

已閱回復(fù)此樓關(guān)注TA 給TA發(fā)消息送TA紅花 TA的回帖

jawang

木蟲 (正式寫手)

應(yīng)助: 3 (幼兒園)
金幣: 3533.7
帖子: 376
在線: 214.7小時
蟲號: 838608

★ ★ ★
小木蟲(金幣+0.5):給個紅包，謝謝回帖
御劍江湖(金幣+2): 謝謝 2011-04-19 10:02:25
Jfreda(金幣+5): 2011-04-19 13:29:55

定義了freegrp就是讓這個原子徹底不動了（當然它可以定義不同方向），而使用define是使這個原子多了一個額外的力，使其保持在原來的位置�？茨阆胍_到的效果吧，如果使用freegrp本人覺得會需要你定義的這些原子位置已經(jīng)平衡了，要不然的話，你還是讓人家動動，調(diào)整下距離比較好點，手冊上說對壓力耦合還有影響

贊一下(2人)

回復(fù)此樓

4樓2011-04-19 09:07:48

已閱回復(fù)此樓關(guān)注TA 給TA發(fā)消息送TA紅花 TA的回帖

Jfreda

鐵蟲 (小有名氣)

應(yīng)助: 0 (幼兒園)
金幣: 21.8
帖子: 91
在線: 31.5小時
蟲號: 870275

怎么又沒人回答了？

贊一下

回復(fù)此樓

5樓2011-04-19 10:53:16

已閱回復(fù)此樓關(guān)注TA 給TA發(fā)消息送TA紅花 TA的回帖

最具人氣熱帖推薦 [查看全部]	作者	回/看	最后發(fā)表

[考研] 0856調(diào)劑，是學校就去 +4	sllhht 2026-03-19	5/250	2026-03-19 17:45 by 星空星月
[考研] 0703化學調(diào)劑，六級已過，有科研經(jīng)歷 +11	曦熙兮 2026-03-15	11/550	2026-03-19 17:13 by yywzz
[考研] 能源材料化學課題組招收碩士研究生8-10名 +4	脫穎而出 2026-03-16	12/600	2026-03-19 16:17 by 脫穎而出
[考研] 0703化學調(diào)劑 +4	18889395102 2026-03-18	4/200	2026-03-19 16:13 by 30660438
[考研] 085600材料與化工調(diào)劑 324分 +10	llllkkkhh 2026-03-18	12/600	2026-03-19 14:33 by llllkkkhh
[考研] 324分 085600材料化工求調(diào)劑 +3	llllkkkhh 2026-03-18	3/150	2026-03-19 14:22 by houyaoxu
[考研] 317求調(diào)劑 +3	申子申申 2026-03-19	6/300	2026-03-19 14:16 by 申子申申
[考研] 0703化學調(diào)劑 +5	pupcoco 2026-03-17	8/400	2026-03-19 13:58 by houyaoxu
[考研] 281求調(diào)劑（0805） +9	煙汐憶海 2026-03-16	19/950	2026-03-19 11:42 by laoshidan
[考研] 化學工程321分求調(diào)劑 +15	大米飯！ 2026-03-15	18/900	2026-03-18 14:52 by haxia
[考研] 303求調(diào)劑 +4	睿08 2026-03-17	6/300	2026-03-18 11:01 by Iveryant
[考研] 275求調(diào)劑 +4	太陽花天天開心 2026-03-16	4/200	2026-03-17 10:53 by 功夫瘋狂
[考研] 278求調(diào)劑 +3	Yy7400 2026-03-13	3/150	2026-03-17 08:24 by laoshidan
[考研] 一志愿，福州大學材料專碩339分求調(diào)劑 +3	木子momo青爭 2026-03-15	3/150	2026-03-17 07:52 by laoshidan
[考研] [導師推薦]西南科技大學國防/材料導師推薦 +3	尖角小荷 2026-03-16	6/300	2026-03-16 23:21 by 尖角小荷
[考研] 304求調(diào)劑 +3	曼殊2266 2026-03-14	3/150	2026-03-16 16:39 by houyaoxu
[考研] 321求調(diào)劑 +5	大米飯！ 2026-03-15	5/250	2026-03-16 16:33 by houyaoxu
[考研] 085600調(diào)劑 +5	漾漾123sun 2026-03-12	6/300	2026-03-16 15:58 by 漾漾123sun
[考研] 0703化學調(diào)劑 290分有科研經(jīng)歷，論文在投 +7	膩膩gk 2026-03-14	7/350	2026-03-16 10:12 by houyaoxu
[考研] 26調(diào)劑/材料科學與工程/總分295/求收留 +9	2026調(diào)劑俠 2026-03-12	9/450	2026-03-13 20:46 by 18595523086