Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation

From: Daniel Roe <>
Date: Thu, 24 Jan 2019 10:50:36 -0500

On Wed, Jan 23, 2019 at 1:32 PM David A Case <> wrote:
> Key is in the (to me) non-obvious arguments to the writedata command:
> script is writing vectors to an output netcdf file ( , but
> stripping the origins of those vectors ("noorigin"), so you just get
> the positions themselves. The script is also preparing a prmtop file
> (comvectors.parm7) that can be used when reading this back into cpptraj
> for further manipulations.
> Note also the "run" command in the middle: one needs to construct all
> the vectors, then essentially start over with the writedata command.
> Also the "chain*" construct will expand to all the chains defined above,
> in this case from chain1 to chain343.
> ....hope this helps...don't be afraid to experiment. One needs to learn
> to "think like Dan does", (or ask him for help) to do some of this.

Indeed, I try to make commands and keywords as user-friendly as
possible while maintaining backwards compatibility with behavior, but
it is not always easy. Feedback on how to improve syntax etc. is very
welcome. Perhaps in this case implementing a dedicated command for
creating a coarse-grained trajectory if that is something people would
find useful.


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Received on Thu Jan 24 2019 - 08:00:06 PST
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