Re: [AMBER] production run duration

From: Ben Roberts <ben.roberts.geek.nz>
Date: Fri, 3 Jun 2011 10:45:07 -0500

Hi Po,

You're in the best position to answer that. The more transitions between different states of interest, the better. Absolute length of time is less important than good sampling, so it all comes down to timescale of motion, and that will vary from protein to protein.

Hope that helps,

Ben

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On 3/06/2011, at 3:53 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Thanks Ben!
> 
> Our loop is 17 residues. What is an advisable duration for that?
> 
> We are actually saving a frame in every 5,000.
> 
> Po
> 
> On Fri, Jun 3, 2011 at 10:32 AM, Ben Roberts <ben.roberts.geek.nz> wrote:
> 
>> 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
>> --
>> For greater security, I support S/MIME encryption.
>> 
>> Sent from my iPhone
>> 
>> 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 Fri Jun 03 2011 - 09:00:04 PDT