It depends on what your sander input file looks like. If your dt = 0.001,
and ntwx=50 (as an example), the coordinates for the structure at 100ps
will be,
100000/(50) = 2000.
The 2000th snapshot in the .mdcrd file corresponds to the lowest energy
structure. You can write a simple .traj input for extracting the
coordinates for this structure as follows:
------------ lowest_traj.in --------------
trajin <name of the .mdcrd file> 2000 2000
trajout lowest pdb
------------------------------------------
Hope this helps. Best,
On Fri, 15 Jun 2007, Seth Lilavivat wrote:
> Dear Amber Community,
>
> If I ran some MD, how would I go about saving the lowest energy
> structure from that particular run? For instance, if I ran 250ps of
> MD and the lowest energy structure was at 100ps, I would like to save
> the coordinates of that particular structure. Thank you for your
> help.
>
> Thanks,
> Seth
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>
--
Ilyas Yildirim
---------------------------------------------------------------
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- University of Rochester - -
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- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Jun 17 2007 - 06:07:35 PDT
