From: Per Larsson (larsson.r.per_at_gmail.com)
Date: Mon May 12 2014 - 13:54:48 CDT
I have a question about dual boost aMD in NAMD. I have read Miao et al, Phys. Chem. Chem. Phys, 2014 as well as Miao, Nichols et al, PNAS, 2014 about how to estimate the boost potential for a membrane system, which seems quite straightforward except for one thing.
When I do dual boost aMD, do the total potential energy and total number of atoms refer to the complete system (i.e. protein+membrane+solvent+ions) or just the bit that is being boosted (presumably), i.e. protein+membrane?
I have a few hundred thousand water molecules, so obviously both the total potential energy and the number of atoms would be hugely different depending on the answer.
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