Re: [AMBER] iwrap=1 or netcdf

From: Jio M <>
Date: Tue, 14 Jan 2014 07:41:21 -0800 (PST)

Dear Daniel

Thanks, one quick question. My earlier simulation upto 50 ns was with iwrap=0 and now I am using netcdf outputs with same iwrap=0. Considering netcdf has much precision; so does that mean I can not "combine" as a regular plot, e.g. some function (say diffusion) vs time, of intial 50ns less precision traj (iwrap=0) with later more precision traj (netcdf).


On Tuesday, January 14, 2014 3:32 PM, Daniel Roe <> wrote:

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.
>AMBER mailing list

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
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Received on Tue Jan 14 2014 - 08:00:03 PST
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