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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » Gromacs/Amber/NAMD » amber 加中性化离子遇到问题
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lifeisall

铜虫 (小有名气)

[求助] amber 加中性化离子遇到问题 已有1人参与

教程上说
(5)加中性化离子：

>addions dna1 Na+ 0  (0意味着中性化)

18 Na+ ions required to neutralize.
Adding 18 counter ions to "dna1" using 1A grid
Grid extends from solute vdw + 1.87  to  7.97
Resolution:      1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 0 sec
Placed Na+ in dna1 at (-0.73, 10.83, 18.51).
Placed Na+ in dna1 at (6.27, -8.17, 18.51).
Placed Na+ in dna1 at (10.27, 4.83, 11.51).
Placed Na+ in dna1 at (-6.73, -8.17, 11.51).
Placed Na+ in dna1 at (-5.73, 3.83, 13.51).
Placed Na+ in dna1 at (-9.73, 3.83, 25.51).
Placed Na+ in dna1 at (6.27, -8.17, 5.51).
Placed Na+ in dna1 at (-5.73, 8.83, 1.51).
Placed Na+ in dna1 at (11.27, 1.83, 25.51).
Placed Na+ in dna1 at (-10.73, -4.17, 28.51).
Placed Na+ in dna1 at (5.27, 3.83, 3.51).
Placed Na+ in dna1 at (2.27, -6.17, 27.51).
Placed Na+ in dna1 at (-10.73, -3.17, 8.51).
Placed Na+ in dna1 at (6.27, 7.83, 15.51).
Placed Na+ in dna1 at (10.27, -3.17, 8.51).
Placed Na+ in dna1 at (-1.73, -12.17, 16.51).
Placed Na+ in dna1 at (-9.73, 3.83, 4.51).
Placed Na+ in dna1 at (-7.73, 8.83, 21.51).
Done adding ions.
产生中性化的prmtop和inpcrd文件：

但是我操作后怎么产生的是如下信息：
> addions dna1 Na+ 0
18 Na+ ions required to neutralize.
Adding 18 counter ions to "dna1" using 1A grid
Grid extends from solute vdw + 4.98  to  11.08
Resolution:      1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 1 sec
Placed Na+ in dna1 at (8.11, -5.38, 12.46).
Placed Na+ in dna1 at (7.11, 6.62, 19.46).
Placed Na+ in dna1 at (-9.89, 9.62, 12.46).
Placed Na+ in dna1 at (-8.89, -10.38, 21.46).
Placed Na+ in dna1 at (0.11, 13.62, 8.46).
Placed Na+ in dna1 at (-13.89, -1.38, 17.46).
Placed Na+ in dna1 at (1.11, -12.38, 12.46).
Placed Na+ in dna1 at (-3.89, 9.62, 25.46).
Placed Na+ in dna1 at (12.11, 2.62, 14.46).
Placed Na+ in dna1 at (-10.89, -5.38, 5.46).
Placed Na+ in dna1 at (-11.89, -2.38, 31.46).
Placed Na+ in dna1 at (12.11, -9.38, 25.46).
Placed Na+ in dna1 at (-8.89, 9.62, -0.54).
Placed Na+ in dna1 at (13.11, -7.38, 0.46).
Placed Na+ in dna1 at (11.11, 9.62, 6.46).
Placed Na+ in dna1 at (3.11, -14.38, 23.46).
Placed Na+ in dna1 at (-11.89, 9.62, 21.46).
Placed Na+ in dna1 at (15.11, -1.38, 29.46).

Done adding ions.

这是什么意思，怎么解决？
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1楼 2014-01-17 10:22:29
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smutao

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★
感谢参与，应助指数 +1
月只蓝: 金币+1, 鼓励交流 2014-01-17 12:36:02
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2楼2014-01-17 10:40:31
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lifeisall

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引用回帖:
2楼: Originally posted by smutao at 2014-01-17 10:40:31
只要done了，就是对了，每次运行加的离子位置不一样是正常的，楼主多虑了。

那 出现charges: 1 sec也正常吗？不应该是charges: 0 sec吗？
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3楼2014-01-17 19:02:17
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smutao

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月只蓝: 金币+1, 鼓励交流 2014-01-18 08:16:14
本帖内容被屏蔽
4楼2014-01-17 19:18:11
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