Re: [AMBER] evaluating physical meaning of Amber results

From: Bozell, Joseph John <>
Date: Wed, 22 Dec 2010 12:55:46 +0000

Hi Richard,

Thanks for the lead...I didn't spot it in the Amber 11 manual (maybe I
have an old version?) but did stumble across the flag description in the
Ambertools documentation.

Back to seeing if I can convince myself that the Amber output is a
reasonable description of reality for self assembly!

I appreciate the help.

Joe Bozell
University of Tennessee

On 12/20/10 6:13 PM, "Richard Owczarzy" <> wrote:

>>C. For experiments 1 and 2 above, I have had the .mdcrd files written in
>>the NetCDF format, per an earlier discussion. I also used NetCDF for
>>experiment 3. However, when I use ptraj for post processing, it appears
>>to convert the files back to ASCII format, since VMD now fails to reload
>>the re->imaged .mdcrd file in NetCDF format. The manual (p. 212) implies
>>that this is what should happen, but is there a flag that could/should
>>be set to keep the files in NetCDF format after the ptraj step? I
>>mention this because it means that my "handling" of each file after the
>>simulation isn't quite identical.
>There is a netcdf flag in trajout command, e.g., trajout <filename>
>netcdf . See page 106 of Amber 11 manual. The default output of trajout
>is in ASCII format.
>Richard Owczarzy
>AMBER mailing list

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Received on Wed Dec 22 2010 - 05:00:07 PST
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