Re: [AMBER] VMD and binary trajectories

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 5 Jun 2014 07:39:54 -0400

On Thu, Jun 5, 2014 at 4:00 AM, James Starlight <jmsstarlight.gmail.com>
wrote:

> Dear Amber users!
>
> I have problems loading my binary trajectories (made with ioutfm=1 option )
> using vmd -crdbox trajectory.mdcrd. How does it possible to work with and
> vizualize such trajectories using vmd? Does it need to be converted in text
> format before loading?
>

‚ÄčThose are NetCDF trajectories, not ASCII mdcrd files with box information.
 -crdbox tells VMD to treat the file as an ASCII mdcrd with box info.

You can either name all NetCDF files with the suffix ".nc" (which is
automatically recognized by VMD and does not require a format flag) or you
can use the "-netcdf" format flag for VMD.

Converting to text format would almost defeat the purpose of NetCDF
trajectories in the first place...

HTH,
Jason
‚Äč
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 05 2014 - 05:00:02 PDT
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