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Jfreda

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[交流] mdrun時(shí)出錯(cuò)

mdrun -s aa.tpr -o aa.trr -c aa.gro &
出現(xiàn)了如下的提示錯(cuò)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(duì)一個(gè)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(wèn)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(qǐng)問(wèn)一下，我應(yīng)該怎么做才是合理的？謝謝！

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1樓 2011-04-18 18:28:08

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Jfreda

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Originally posted by jawang at 2011-04-19 09:07:48:
定義了freegrp就是讓這個(gè)原子徹底不動(dòng)了（當(dāng)然它可以定義不同方向），而使用define是使這個(gè)原子多了一個(gè)額外的力，使其保持在原來(lái)的位置�？茨阆胍_(dá)到的效果吧，如果使用freegrp本人覺(jué)得會(huì)需要你定義的這些原子位 ...

好的，非常感謝！

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6樓2011-04-19 13:30:13

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jawang

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小木蟲(chóng)(金幣+0.5):給個(gè)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(wèn)題的吧，只跑了32步。

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

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2樓2011-04-18 18:42:24

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Jfreda

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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(wèn)一下freegroup和define有什么區(qū)別嗎？我的目的是在優(yōu)化的過(guò)程中逐步放開(kāi)限制。

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3樓2011-04-18 19:10:46

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jawang

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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(gè)原子徹底不動(dòng)了（當(dāng)然它可以定義不同方向），而使用define是使這個(gè)原子多了一個(gè)額外的力，使其保持在原來(lái)的位置�？茨阆胍_(dá)到的效果吧，如果使用freegrp本人覺(jué)得會(huì)需要你定義的這些原子位置已經(jīng)平衡了，要不然的話(huà)，你還是讓人家動(dòng)動(dòng)，調(diào)整下距離比較好點(diǎn)，手冊(cè)上說(shuō)對(duì)壓力耦合還有影響

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4樓2011-04-19 09:07:48

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