Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files?

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 30 Apr 2014 11:55:26 -0400

On Wed, 2014-04-30 at 23:45 +0800, Yip Yew Mun wrote:
> I tried the method, but my trajectory is 5000 frames long, and when I
> ran it, it gave me very huge energies. But when I do it frame by
> frame, the energies are normal looking.

Then you probably made a mistake with box information (did you use
"nobox" when you shouldn't have or did you not use "nobox" when you
should have?)

Try using NetCDF trajectories and setting ioutfm=1 in the sander input
file. 

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 30 2014 - 09:00:04 PDT
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