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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 » NAMD问题
北京石油化工学院2026年研究生招生接收调剂公告
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柯艳萍

铜虫 (初入文坛)

[求助] NAMD问题 已有1人参与

NAMD在生成日志文件的时候出现如下错误，怎么解决啊？本人是新手，照着教程做的，望高手指教，感激不尽！
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 702!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 26!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 530!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1342!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1257!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 372!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 712!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 52!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4926!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1306!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4311!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5406!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5372!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2186!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2272!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5457!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3748!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2777!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2462!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3037!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2957!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3370!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================

WallClock: 79.281998  CPUTime: 79.280998  Memory: 89.121094 MB
Program finished.
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1楼 2014-04-24 10:33:19
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yylcx

金虫 (正式写手)

【答案】应助回帖

★ ★ ★ ★ ★ ★
感谢参与，应助指数 +1
柯艳萍: 金币+5 2014-04-24 17:59:19
月只蓝: 金币+1, 感谢指导！ 2014-04-24 18:29:03
你试一下把约束系数改小一点，或许有用。
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2楼2014-04-24 10:40:59
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niuyuzhen110

新虫 (初入文坛)
力场错误
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3楼2014-04-24 11:14:11
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柯艳萍

铜虫 (初入文坛)
引用回帖:
2楼: Originally posted by yylcx at 2014-04-24 10:40:59
你试一下把约束系数改小一点，或许有用。

谢谢回复啊，能不能说清楚一点啊，什么是约束系数啊，本人菜鸟一个
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4楼2014-04-24 18:00:51
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yylcx

金虫 (正式写手)
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月只蓝: 金币+1, 鼓励交流！ 2014-04-25 17:59:07
引用回帖:
4楼: Originally posted by 柯艳萍 at 2014-04-24 18:00:51
谢谢回复啊，能不能说清楚一点啊，什么是约束系数啊，本人菜鸟一个...

我也不是很会，你是用下面这个来约束原子么？
constraints                on
consref                        constr.pdb
conskfile                constr.pdb
conskcol                B
constraintscaling        10.0


如果是的话你试试把最后一行constraintscaling的数值改小一点
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5楼2014-04-24 18:57:01
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柯艳萍

铜虫 (初入文坛)
引用回帖:
3楼: Originally posted by niuyuzhen110 at 2014-04-24 11:14:11
力场错误

谢谢啊，能不能说的清楚一点啊？应该怎么办啊
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6楼2014-04-25 08:58:03
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柯艳萍

铜虫 (初入文坛)
引用回帖:
5楼: Originally posted by yylcx at 2014-04-24 18:57:01
我也不是很会，你是用下面这个来约束原子么？
constraints                on
consref                        constr.pdb
conskfile                constr.pdb
conskcol                B
constraintscaling        10.0


如果是的话你试试把最后一行constraintscaling的数值改 ...

我是用的教程里下的软件包namd-tutorial-files里的ubq_ws_eq.conf来生成的，ubq_ws_eq.conf这个文件是不是得自己做啊？该怎么做？谢谢啦
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7楼2014-04-25 09:05:47
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yylcx

金虫 (正式写手)
内容已删除
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8楼2014-04-25 15:38:50
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