I start from a quite valid folded state of the protein...<br><br><div><span class="gmail_quote">On 1/17/06, <b class="gmail_sendername">David Mobley</b> <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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. <br>
<br>
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. :)<br><span class="sg">
<br>
David<br>
<br><br></span><div><span class="q"><span class="gmail_quote">On 1/17/06, <b class="gmail_sendername">Tamas Horvath</b> <<a href="mailto:hotafin@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
hotafin@gmail.com</a>> wrote:</span></span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><span class="q">
How may I check when a system reached it's equilibrium?<br>
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