24小时热门版块排行榜    

查看: 1224  |  回复: 7
当前主题已经存档。
当前只显示满足指定条件的回帖,点击这里查看本话题的所有回帖

jings

金虫 (正式写手)

[交流] 【求助】MD关于平衡的问题 已有2人参与

我在建立模型的时候,用discovery动力学平衡,但是我不知道如何选取合适的dynamics time,一般现在很多人都用1ns,但是如果体系太大,选择这个时间运算会很长,我想缩短一点时间,请问有谁知道怎么从平衡图上面看出体系已经达到了平衡啊?
回复此楼

» 猜你喜欢

跳舞吧!如同没有任何人注视你一样。去爱吧!如同从来没有受过伤害一样。歌唱吧!如同没有人聆听一样。工作吧!如同不需要金钱一样。活着吧!如同今日是末日一
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

linxi1454

银虫 (正式写手)

★ ★ ★ ★
jings(金币+5):可以加个qq么?57790934,我还不是太懂,想具体问一下你,谢谢了 2010-04-02 10:17
ghcacj(金币+4):谢谢 2010-04-02 10:26
当然,这只是一个很粗略的标记,具体可以参考如下

How to check when a system reaches it's equilibrium

This is a nontrivial question, and the answer partly depends on what you are trying to do. As David points out, if you want to do protein folding, say, your protein needs to have long enough to forget about its starting state (hence his comment about folding and unfolding). Usually that takes a prohibitively long time, though, for large proteins. So assuming you don't want to solve the protein folding problem you have to be content with something less. Definitely you want to run long enough that the protein RMSD  quits increasing, temperature and energy begin fluctuating around some relatively stable value, and so on. You can also look for things like number of protein-water hydrogen bonds if you have explicit solvent; this tends to take a much longer time to equilibrate. Probably a good suggestion is to find out what other people have done who are doing something similar to you, and make sure you equilibrate at least as much as they do.

    Just a remark about the rmsd with respect to the Xray structure: you might want to plot rmsd vs log(time), that is a better check sometimes.

    Well, rmsd is not that bad. Just that it is easier to judge a converged rmsd from a non-converged one when you plot it against log(t) instead of t. Another convergence check is the cosine content of the traj projected onto some (slow) PCA modes.

详细的可以参考这里 http://www.mdbbs.org/viewthread. ... ghlight=equilibrium
3楼2010-04-02 10:05:18
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
查看全部 8 个回答

linxi1454

银虫 (正式写手)

★ ★
ghcacj(金币+2):谢谢 2010-04-02 10:04
你输出系统的potential energy,如果收敛了就说明达到平衡了,你可以设置跑1ns,或者更长,隔一段时间查看一下pe是否收敛
2楼2010-04-02 10:02:59
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

linxi1454

银虫 (正式写手)

★ ★
ghcacj(金币+2):谢谢 2010-04-02 10:26
收敛,就是某个时刻以后系统只在平均值附近涨落,涨落肯定是有的,需要根据你具体的物理量来分析,关于涨落你可以不关心,你可以这么比较
比如1ns以后系统收敛了,那么1ns-1.5ns和1.5ns到2ns之间的平均是应该近似相等的
4楼2010-04-02 10:09:25
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

jings

金虫 (正式写手)

麻烦具体给我一下怎么计算平均值的作法吧。我刚刚学习这个软件,还不是特别明白。谢谢哈
跳舞吧!如同没有任何人注视你一样。去爱吧!如同从来没有受过伤害一样。歌唱吧!如同没有人聆听一样。工作吧!如同不需要金钱一样。活着吧!如同今日是末日一
5楼2010-04-02 10:27:45
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
普通表情 高级回复 (可上传附件)
最具人气热帖推荐 [查看全部] 作者 回/看 最后发表
[考研] 梁成伟老师课题组欢迎你的加入 +8 一鸭鸭哟 2026-03-14 9/450 2026-03-16 17:35 by 沐霖12138
[考研] 0703化学调剂 ,六级已过,有科研经历 +7 曦熙兮 2026-03-15 7/350 2026-03-16 16:34 by houyaoxu
[考研] 312求调剂 +3 陌宸希 2026-03-16 4/200 2026-03-16 15:06 by peike
[考研] 255求调剂 +3 李嘉慧, 2026-03-12 4/200 2026-03-14 16:58 by 有只狸奴
[考研] 复试调剂 +3 呼呼?~+123456 2026-03-14 3/150 2026-03-14 16:53 by WTUChen
[考研] 290求调剂 +4 @将就将就看 2026-03-10 8/400 2026-03-14 14:23 by 千千运气
[考研] 331求调剂(0703有机化学 +5 ZY-05 2026-03-13 6/300 2026-03-14 10:51 by Jy?
[考研] 0703求调剂 +7 jtyq001 2026-03-10 7/350 2026-03-14 01:06 by JourneyLucky
[考研] 285 求调剂 资源与环境 一志愿北京化工大学 +3 未名考生 2026-03-10 3/150 2026-03-13 23:04 by JourneyLucky
[考研] 0703,333分求调剂 一志愿郑州大学-物理化学 +3 李魔女斗篷 2026-03-11 3/150 2026-03-13 22:24 by JourneyLucky
[考研] 材料与化工求调剂一志愿 985 总分 295 +8 dream…… 2026-03-12 8/400 2026-03-13 22:17 by 星空星月
[考研] 0703化学一志愿211 总分320求调剂 +5 玛卡巴卡啊哈 2026-03-11 5/250 2026-03-13 21:40 by JourneyLucky
[考研] (081700)化学工程与技术-298分求调剂 +12 11啦啦啦 2026-03-11 35/1750 2026-03-13 21:25 by JourneyLucky
[考研] 281求调剂 +9 Koxui 2026-03-12 11/550 2026-03-13 20:50 by Koxui
[考研] 26调剂/材料科学与工程/总分295/求收留 +9 2026调剂侠 2026-03-12 9/450 2026-03-13 20:46 by 18595523086
[考研] 290求调剂 +7 ADT 2026-03-12 7/350 2026-03-13 15:17 by JourneyLucky
[考研] 08食品或轻工求调剂,本科发表3篇sci一区top论文,一志愿南师大食品科学与工程 +3 我是一个兵, 2026-03-10 3/150 2026-03-13 10:21 by Yuyi.
[考研] 290求调剂 +3 ADT 2026-03-13 3/150 2026-03-13 10:19 by peike
[考研] 化工学硕306求调剂 +9 42838695 2026-03-12 9/450 2026-03-13 10:16 by houyaoxu
[考研] 收调剂 +7 调剂的考研学生 2026-03-10 7/350 2026-03-10 17:57 by 麦茶汤圆
信息提示
请填处理意见