| 查看: 1142 | 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 | |||
[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
请问有评职称，把科研教学业绩算分排序的高校吗
已经有6人回复
-
2025冷门绝学什么时候出结果
已经有6人回复
-
Bioresource Technology期刊，第一次返修的时候被退回好几次了
已经有7人回复
-
真诚求助：手里的省社科项目结项要求主持人一篇中文核心，有什么渠道能发核心吗
已经有8人回复
-
寻求一种能扛住强氧化性腐蚀性的容器密封件
已经有5人回复
-
请问哪里可以有青B申请的本子可以借鉴一下。
已经有4人回复
-
请问下大家为什么这个铃木偶联几乎不反应呢
已经有5人回复
-
天津工业大学郑柳春团队欢迎化学化工、高分子化学或有机合成方向的博士生和硕士生加入
已经有4人回复
-
康复大学泰山学者周祺惠团队招收博士研究生
已经有6人回复
-
AI论文写作工具：是科研加速器还是学术作弊器？
已经有3人回复
5楼2010-04-02 10:27:45
2楼2010-04-02 10:02:59
★ ★ ★ ★
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
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
4楼2010-04-02 10:09:25