Re: [AMBER] Fwd: About long simulation

From: Daniel Roe <>
Date: Thu, 17 Feb 2011 08:25:28 -0500


On Wed, Feb 16, 2011 at 7:18 PM, Jason Swails <> wrote:
> The main precautions to take are:
> 1) Use iwrap=1 so that coordinates don't overflow the restart format limit.
> 2) Recognize that this can cause visualization artifacts resulting from the
> imaging.
> 3) Center and image your trajectory to get things fitted the way you want
> them.

In addition to the three points that Jason mentions, I would recommend
using the Netcdf trajectory format (ioutfm=1). It is more compact,
faster to process, and less error-prone than the ASCII format.


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Received on Thu Feb 17 2011 - 05:30:04 PST
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