24小时热门版块排行榜    

北京石油化工学院2026年研究生招生接收调剂公告
查看: 1249  |  回复: 7

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.
回复此楼

» 猜你喜欢

已阅   关注TA 给TA发消息 送TA红花 TA的回帖

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
已阅   关注TA 给TA发消息 送TA红花 TA的回帖

niuyuzhen110

新虫 (初入文坛)

力场错误
3楼2014-04-24 11:14:11
已阅   关注TA 给TA发消息 送TA红花 TA的回帖

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
已阅   关注TA 给TA发消息 送TA红花 TA的回帖

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
已阅   关注TA 给TA发消息 送TA红花 TA的回帖

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
6楼2014-04-25 08:58:03
已阅   关注TA 给TA发消息 送TA红花 TA的回帖

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
已阅   关注TA 给TA发消息 送TA红花 TA的回帖

yylcx

金虫 (正式写手)

内容已删除
8楼2014-04-25 15:38:50
已阅   关注TA 给TA发消息 送TA红花 TA的回帖
相关版块跳转 我要订阅楼主 柯艳萍 的主题更新
最具人气热帖推荐 [查看全部] 作者 回/看 最后发表
[考研] 土木水利328分求调剂 +6 疾风知劲草666 2026-04-02 6/300 2026-04-03 11:38 by znian
[考研] 求调剂,一志愿南京航空航天大学 ,080500材料科学与工程学硕 +4 @taotao 2026-04-03 4/200 2026-04-03 11:13 by 无际的草原
[考研] 282求调剂 +3 aaa车辆 2026-04-02 3/150 2026-04-02 21:55 by zllcz
[考研] 362求调剂 +14 西南交材料专硕3 2026-03-31 14/700 2026-04-02 17:50 by yunlongyang
[考研] 346求调剂 +5 郑诚乐 2026-04-02 5/250 2026-04-02 16:38 by SZW_UJN
[考研] 一志愿同济大学323分(080500)求调剂 +6 yikeniu 2026-04-01 6/300 2026-04-02 14:19 by smileboy2006
[考研] 282求调剂 +13 呼吸都是减肥 2026-04-01 13/650 2026-04-02 14:10 by baoball
[考研] 找调剂 +6 楚乔乔 2026-04-01 6/300 2026-04-02 12:06 by xiaoranmu
[考研] 272求调剂,接受跨专业调剂! +4 闲鱼卢 2026-03-31 4/200 2026-04-02 11:18 by guyan1000
[考研] 英一数一408,总分284,二战真诚求调剂 +12 12.27 2026-03-30 14/700 2026-04-02 00:18 by 欣喜777
[考研] 材料调剂 +14 一样YWY 2026-04-01 14/700 2026-04-01 21:07 by lijunpoly
[考研] 070300一志愿211,312分求调剂院校 +14 小黄鸭宝 2026-03-30 14/700 2026-04-01 20:19 by 赖春艳
[考研] 353求调剂 +4 拉钩不许变 2026-04-01 4/200 2026-04-01 18:10 by 记事本2026
[考研] 318求调剂 +8 七忆77 2026-04-01 8/400 2026-04-01 10:37 by Jaylen.
[考研] 339求调剂 +5 zjjkt 2026-03-31 5/250 2026-04-01 09:18 by JourneyLucky
[考研] 一志愿华东师范大学有机化学专业,初试351分,复试被刷求调剂! +9 真名有冰 2026-03-29 10/500 2026-03-31 18:01 by xhai2011
[考研] 材料与化工272求调剂 +25 阿斯蒂芬2004 2026-03-28 25/1250 2026-03-31 16:27 by hypershenger
[考研] 085601 329分调剂 +6 yzsa12 2026-03-31 6/300 2026-03-31 15:23 by yanflower7133
[考研] 求佛 +7 迷人的哈哈 2026-03-28 7/350 2026-03-28 16:47 by 催化大白
[考研] 一志愿南京航空航天大学材料学硕求调剂 +3 @taotao 2026-03-28 3/150 2026-03-28 10:26 by JourneyLucky
信息提示
请填处理意见