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
_______________________________________________
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 Sat Apr 17 2010 - 10:00:02 PDT
