Re: [AMBER] FW: about trajectory unwrap

From: Daniel Roe <>
Date: Wed, 10 Sep 2014 09:32:50 -0600


The 'unwrap' and 'image' commands have the opposite effect, so
effectively all you are doing here is cancelling out your 'unwrap'
with your 'image'. If all you want is to center on your first molecule
and re-image I recommend trying 'autoimage'. Also, it's better to
'strip' prior to imaging since this results in the code having to deal
with far less molecules (so it will be faster). For example:

trajin ../../ 3000 4000
strip :WAT,Na+
autoimage origin
trajout macro_prod1_noWAT2.mdcrd

Hope this helps,


On Wed, Sep 10, 2014 at 9:06 AM, Kong, Ren <> wrote:
> Hi all,
> I ran a 4 ns MD simulation and did the RMSD analysis. I found a few frames having very large RMSD, such as 27.4 Å while the others were normal (~3 Å).
> I thought it would be the discontinued trajectory problem as I used IWRP=1 in MD input file.
> Then I used following commands in order to map the frames to the original cell according to the AmberTools manual:
> trajin ../../ 3000 4000
> trajout macro_prod1_noWAT2.mdcrd
> unwrap :1-259 ### 1-259 is the number of residues of the protein in my simulation system.
> center :1-259 mass origin
> image center origin familiar
> strip :WAT,Na+
> go
> However, after all these steps, I still got the trajectory with some of frames having large RMSD (27.4 Å).
> And when I viewed the output trajectory by VMD, I found the protein jumped out of view for a while.
> Could anyone tell me how to get a continuous trajectory?
> Thanks a lot.
> Best,
> Ren Kong
> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties and designated as a Magnet hospital for excellence in nursing. Houston Methodist has also been named to FORTUNE® Magazine's "100 Best Companies to Work For®" list for nine years in a row. Visit us at Follow us at and ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
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Received on Wed Sep 10 2014 - 09:00:03 PDT
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