Re: Dual boost accelerated md energy parameters?

From: Thomas Evangelidis (
Date: Mon May 12 2014 - 14:11:45 CDT

Total number of *real* atoms. I.g. if you use TIP4P-Ew you should count 3
atoms per molecule.

On 12 May 2014 21:54, Per Larsson <> wrote:

> Dear users
> 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.
> Thanks
> /Per

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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