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【求助】MD关于平衡的问题 已有2人参与
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| 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? |
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4楼2010-04-02 10:09:25
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
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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
5楼2010-04-02 10:27:45