Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Dec 16 2010 - 07:04:19 CST

Dear Jrme,

>That *is* a full turn :-)
Amm, yes, of course, sorry, it was toward the end of a long day :)

>Actually 3700000, including the last stage, which repeats the first
>one (useful to check for hysteresis). 10000 steps might not be needed
>for convergence, but the restraints seem to make it slower than a
>standard minimization.

Just one more question: What happens when the transition from one stage to
the next occurs? I would imagine that only the reaction coordinate increases
for one step, but the rest of the system stays minimized (since the last
frame of the previous stage is minimized).

>No idea. You should post this as a separate message, because no one
is going to notice it in here.
Oh well, at least they won't see me miscounting the difference between -70
and 290 :)

Thank you for your help,
Ajasja

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