Re: [AMBER] significance of time-average or representative structures from MD

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 5 Sep 2010 22:28:49 -0400

Hello,

You can cluster your snapshots and extract representative snapshots.
Another approach is to find the energy of every snapshot (you can do this by
setting imin=5 and setting maxcyc=1, as described in the manual), and then
choosing the lowest energy snapshots to run QM/MM calculations on. The
average structure, however, will have rotationally degenerate atoms
superimposed on one another, and may be quite distorted.

Good luck!
Jason

On Sun, Sep 5, 2010 at 2:01 PM, Senthil Natesan <sen.natesan.yahoo.com>wrote:

>
> Dear Amber Users/Developers,
>
> I would be very thankful if you can share the significance and various uses
> of
> time-average or representative structures from MD simulation.
> I use it for QM/MM energy calculations.
>
> I hope that Amber users/developers will kindly share their experiences to
> enrich us (the beginners).
>
> I consider this forum as a great learning place, in addition to getting
> suggestions/fixes
> to successfully use AMBER
>
> Thanks in advance !!.
>
> Senthil Natesan
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Sep 05 2010 - 19:30:04 PDT
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