Jason, thanks for the reply.
But my question was to learn what are other possible uses of a representative
structure
from MD simulation?.
thanks,
Senthil
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sun, September 5, 2010 10:28:49 PM
Subject: Re: [AMBER] significance of time-average or representative structures
from MD
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 06 2010 - 14:30:03 PDT
