Re: [AMBER] Trajectory Smoothing

From: Ganesh Krishnan <>
Date: Sat, 17 Apr 2010 09:43:41 -0700 (PDT)

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 <> wrote:

From: Bill Ross <>
Subject: Re: [AMBER] Trajectory Smoothing
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.


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