From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Thu Feb 14 2013 - 12:30:39 CST
This question is a bit more philosophically motivated than a lot of things that hit this list, but I was hoping to get some valuable input. At the BPS meeting the beginning of this month, I was talking with a fellow that feels that questions the value of explicit solvent simulations in PBC on unfolded proteins (and I guess to some degree folded structures). The basis of this was the fact that you'd need to use an enormous water box to avoid any impact from the inherently restricted volume in these simulations. Intuitively, I feel that this wouldn't impact any but the rarest of confirmations, but honestly don't feel like I have seen much quantified information about these effects – or even a lot of speculation in literature.
If anyone has an opinion they'd like to share I'd appreciate it. Also, if there is any literature I've missed I'd love to read it.
Thanks a lot,
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