Re: [AMBER] GPU accelerated - accelerated MD (Was: Count number of frames in any trajectory file)

From: Ross Walker <>
Date: Mon, 15 Oct 2012 22:44:07 +0200

Hi Shashidhar,

I appreciate the confusion, accelerated MD is an unfortunate name.
Essentially the is GPU accelerated MD which is the use of GPUs to run MD
simulations faster.

Andreas W. Goetz; Mark J. Williamson; Dong Xu; Duncan Poole; Scott Le
Grand; & Ross C. Walker* "Routine microsecond molecular dynamics
simulations with AMBER - Part I: Generalized Born", J. Chem. Theory
Comput.,2012, 8 (5), pp 1542-1555 , DOI: 10.1021/ct200909j

Scott Le Grand; Andreas W. Goetz; & Ross C. Walker* "SPFP: Speed without
compromise - a mixed precision model for GPU accelerated molecular
dynamics simulations.", Comp. Phys. Comm, 2012, (in press,

Then there is accelerated MD (aMD) which is a method for sampling phase
space faster by modifying the underlying potential. This aMD can be run on
either CPU or GPU. In the case of running it on the GPU one could
conceivably call it GPU accelerated^2 MD. ;-) Or perhaps GPU accelerated
aMD would be the best acronym. See:

Pierce, L.C.T., Salomon-Ferrer, R. de Oliveira, C.A.F. McCammon, J.A.
Walker, R.C., "Routine access to millisecond timescale events with
accelerated molecular dynamics.", Journal of Chemical Theory and
Computation, 2012, in press, DOI: 10.1021/ct300284c

In summary though they are distinctly different things. Support for aMD
(on CPU and GPU in PMEMD) was added as part of AMBER 12. You will need to
be able to upgrade to AMBER 12 in order to use it. For a recent review of
AMBER 12 and the new features available see:

Salomon-Ferrer, R.; Case, D.A.; Walker, R.C.; "An overview of the Amber
biomolecular simulation package", WIREs Comput. Mol. Sci., 2012, in press,
DOI: 10.1002/wcms.1121 <>

Hope that helps.

All the best

On 10/15/12 10:14 PM, "Shafinaz Chowdhury" <>

>Dear Dr. Roe
>Is GPU accelerated MD and accelerated MD using a bias potential function
>are same ? GPU accelerated MD is available in amber11. I have amber11.
>Please let me know? Do you have any input file or instruction so that I
>try this technique.
>Thanks in advance.
>Shafinaz Chowdhury
>AMBER mailing list

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Received on Mon Oct 15 2012 - 14:00:03 PDT
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