AMBER Archive (2007)

Subject: Re: AMBER: Saving a structuring from trajectory

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Jun 15 2007 - 13:59:50 CDT


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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