Re: [AMBER] iwrap=1 or netcdf

From: Daniel Roe <>
Date: Tue, 14 Jan 2014 08:31:02 -0700


You should definitely use NetCDF trajectories since they have better
precision and are faster to process. Note that you can also post-process an
imaged trajectory with the 'unwrap' command; this will make the trajectory
as if you had simulated with iwrap=0.

Hope this helps,


On Tue, Jan 14, 2014 at 6:10 AM, Jio M <> wrote:

> Dear All
> My system atoms has diffused very far so getting **** in coordinates. If I
> am not wrong iwrap=1 put things back in original unit cell. Though I think
> if I need all track of diffusion then I should use netcdf option (please
> correct me). I have run just 50 ns and need to go much longer.
> I know only about diffusion analysis which can/should not be performed on
> trajectories obtained by iwrap=1. Just for future purpose I am curious to
> know what kind analysis I can NOT perform if I use iwrap=1. But ofcourse I
> would need to study diffusion things so I should use netcdf format.
> thanks
> Jiom
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jan 14 2014 - 08:00:02 PST
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