sure... rmsd in itself is not very meaningful...<br><br><div><span class="gmail_quote">On 1/18/06, <b class="gmail_sendername">Lars Schaefer</b> <<a href="mailto:Lars.Schaefer@mpi-bpc.mpg.de">Lars.Schaefer@mpi-bpc.mpg.de
</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;"><br>Hi Tamas,<br>just a remark about the rmsd with respect to the Xray structure: you
<br>might want to plot rmsd vs log(time), that is a better check sometimes.<br>Cheers,<br>Lars<br><br><br><br>Tamas Horvath wrote:<br><br>> I start from a quite valid folded state of the protein...<br>><br>> On 1/17/06, *David Mobley* <
<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a><br>> <mailto:<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>>> wrote:<br>><br>> This is a nontrivial question, and the answer partly depends on
<br>> what you are trying to do. As David points out, if you want to do<br>> protein folding, say, your protein needs to have long enough to<br>> forget about its starting state (hence his comment about folding
<br>> and unfolding). Usually that takes a prohibitively long time,<br>> though, for large proteins. So assuming you don't want to solve<br>> the protein folding problem you have to be content with something
<br>> less. Definitely you want to run long enough that the protein RMSD<br>> quits increasing, temperature and energy begin fluctuating around<br>> some relatively stable value, and so on. You can also look for
<br>> things like number of protein-water hydrogen bonds if you have<br>> explicit solvent; this tends to take a much longer time to<br>> equilibrate.<br>><br>> Probably a good suggestion is to find out what other people have
<br>> done who are doing something similar to you, and make sure you<br>> equilibrate at least as much as they do. :)<br>><br>> David<br>><br>><br>> On 1/17/06, *Tamas Horvath* < <a href="mailto:hotafin@gmail.com">
hotafin@gmail.com</a><br>> <mailto:<a href="mailto:hotafin@gmail.com">hotafin@gmail.com</a>>> wrote:<br>><br>> How may I check when a system reached it's equilibrium?<br>><br>> _______________________________________________
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