Re: Selective accelerated MD in NAMD

From: Alexander Adams (
Date: Sat Apr 07 2018 - 07:00:37 CDT

Hi Chitrak,

I believe these are the relevant papers.

Selective aMD in Desmond:
Wereszczynski, J. & McCammon, J. A. Using selectively applied accelerated
molecular dynamics to enhance free energy calculations. J. Chem. Theory
Comput. 6, 3285–3292 (2010).

Selective aMD in Amber:
Doshi, U., McGowan, L. C., Ladani, S. T. & Hamelberg, D. Resolving the
complex role of enzyme conformational dynamics in catalytic function. Proc.
Natl. Acad. Sci. 109, 5699–5704 (2012).

Review article of advances in aMD that directed me to these articles:
Doshi, U. & Hamelberg, D. Towards fast, rigorous and efficient
conformational sampling of biomolecules: Advances in accelerated molecular
dynamics. Biochim. Biophys. Acta - Gen. Subj. 1850, 878–888 (2015).

Hope this helps,

On Fri, Apr 6, 2018 at 6:42 PM, Chitrak Gupta <> wrote:

> Hi Alexander,
> I was not aware that you could do accelerated MD on a part of your system--000000000000d90d59056940ebc1--

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