Re: [AMBER] production run duration

From: Ben Roberts <ben.roberts.geek.nz>
Date: Fri, 3 Jun 2011 00:02:36 -0500

Hi Po,

You probably want a good deal more than 10 ns. Somewhere between 50 and 100 is probably a good start, especially since - depending on the size of your loop - it may be a relatively slow motion.

As for saving the trajectory, saving one frame in 1,000 (which is what it sounds as though you're doing) is fairly conventional, though you could afford to save maybe one in 2,000 or one in 5,000.

Cheers,
Ben

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On 2/06/2011, at 11:46 PM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Hi all!
> 
> i am trying to study the flexibility in the loop region of protein. what is
> the ideal time duration of the production run that i should employ? i have
> already tried 10 ns, is that sufficient?
> Also, i am generating co-ordinates every 10ps. what is the significance of
> increasing or decreasing that number?
> 
> Thanks!
> 
> Po
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Received on Thu Jun 02 2011 - 22:30:02 PDT