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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 05 2010 - 19:30:04 PDT
