Re: [AMBER] evaluating physical meaning of Amber results

From: Richard Owczarzy <>
Date: Mon, 20 Dec 2010 23:13:54 +0000

>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
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Received on Mon Dec 20 2010 - 15:30:03 PST
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