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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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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
7楼2014-04-25 09:05:47
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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。
2楼2014-04-24 10:40:59
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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
4楼2014-04-24 18:00:51
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yylcx

金虫 (正式写手)


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
5楼2014-04-24 18:57:01
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