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.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:24 CST