yes there is an explicit procedure, you change temp0 using the
weight change section of the input file. It can be varied over multiple
ranges during the MD run. Check p 106 of the Amber9 manual. I find
it quite flexible and convenient.
On 6/26/07, Hayden Eastwood <s0237717.sms.ed.ac.uk> wrote:
>
>
> Hullo Jem
>
> There is no implicit procedure within AMBER (that I know of) for
> performing
> simulated annealing. I usually do it by writing a shell script that
> performs
> hot MD, followed by various cooling steps that the shell script defines
> with
> a function of my choice (often exponential or random). I would recommend
> doing it like that.
>
> Best
>
> Hayden
>
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of
> Joseph Maxwell
> Sent: 26 June 2007 00:28
> To: amber.scripps.edu
> Subject: AMBER: Simulated Annealing
>
> Hello,
>
> Can AMBER be set up for Simulated Annealing? Could not seem to see it in
> the
> manual.
>
> Thanks
>
> --jem--
>
>
> ________________________________
>
> Make every IM count. Download Windows Live Messenger and join the i'm
> Initiative now. It's free. Make it count!
> <http://im.live.com/messenger/im/home/?source=TAGWL_June07>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 27 2007 - 06:07:31 PDT
