Hi,
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,
-Dan
On Tue, Jan 14, 2014 at 6:10 AM, Jio M <jiomm.yahoo.com> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 14 2014 - 08:00:02 PST
