You can post-process the trajectory with sander using the imin==5 option and
setting maxcyc to the number of steps you want to minimize for. If you set
ntwx to a non-zero value the minimized frames will be written to whatever
file is specified by '-x'.
-Dan
On Sat, Apr 17, 2010 at 12:43 PM, Ganesh Krishnan <hereisganesh.yahoo.com>wrote:
> How do I energy minimize each frame? As far as I understand, the minimize
> option in sander takes a restrt file (one frame) and minimizes that. Do you
> mean that I generate restrt files for each frame, minimize each of those and
> recombine them? Thanks for your help.
>
> --- On Thu, 4/15/10, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Trajectory Smoothing
> To: amber.ambermd.org
> Date: Thursday, April 15, 2010, 7:47 AM
>
> > I find that smoothing all the residues results in
> > unwanted geometric distortions
>
> If you energy minimize each frame of the smoothed trajectory,
> this should clean it up.
>
> > So I am looking at smoothing selected residues.
>
> I doubt that is possible with current software.
>
> Bill
>
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--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Sat Apr 17 2010 - 14:00:02 PDT
