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 - 02:00:02 PDT
