Hi,
Hi Andrea,
I think it's a good thing to start another simulation by mutating the
[EMAIL PROTECTED] Besides, it would be good to mutate the [EMAIL PROTECTED]
back, to
see if it goes the other way. In any case, you'll have to perform
multiple simulations. For a strategy on comparing simulations, to see
which properties are affected, you can have a look at chapters 2 and 4
of my thesis, which I know you have. Comparing with respect to the
"internal dynamics" by means of PCA is also a good possibility and
would generally be approached by "Combined Essential Dynamics", but I
would note there are better methods.
In addition to that I would like to mention that you should be careful
when comparing simulations by using PCA. The conformational states
obtained by PCA may be artificial ones. I have discussed this problem in
the recent paper: Proteins 65, 898, 2006. I don't want to advertise the
paper but just try to provide more information which may help you more.
Best wishes,
Phuong
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