Re: [AMBER] Difference of two trajectories

From: Daniel Roe <>
Date: Mon, 1 Aug 2016 11:27:33 -0600


If what you're interested in are atomic fluctuations you can use the
'atomicfluct' command to calculate them within each reference frame.
See the manual for more details.


On Wed, Jul 20, 2016 at 3:25 PM, C.D. Okafor <> wrote:
> Hello,
> I was wondering if there is a way in AMBER to 'subtract' two trajectories, to obtain a difference between the two sets of coordinates.
> What I'm trying to do: I have run simulations on a multi-domain protein and I have aligned the protein two ways: 1) overall with respect to a reference to remove translations and rotations, and 2) with respect to just one domain. I'm interested in this one domain and somehow looking at the difference between overall fluctuations and fluctuations with this one domain. It seems like the way to do this would be to subtract the two and analyze the difference trajectory. I have not been able to find a way to do this yet.
> Any thoughts would be appreciated.
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Aug 01 2016 - 10:30:04 PDT
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