On Mon, Dec 9, 2013 at 3:17 AM, Ibrahim Said <saidibrahim569.gmail.com>wrote:
> Dear Amber users
> I am planning to run an accelerated molecular dynamics simulations for some
> proteins to find out the metastate of these proteins. I have Amber12 but I
> do not know the commands should I use in sander and pmemd . Any help will
> be appreciated.
>
The Amber12 manual is a good place to start. Accelerated molecular
dynamics is listed in the table of contents, on page 160. Some of the text
runs off the page, but it should be enough to get you started.
You should also read the original papers from the McCammon group, as that
will explain how to reweight the resulting simulations to obtain Boltzmann
statistics.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 09 2013 - 04:30:03 PST
