Hi,
As long as the initial ASCII trajectory is not corrupt (i.e. does not
contain ****) you can use it with the subsequent NetCDF trajectory without
issue.
-Dan
On Tue, Jan 14, 2014 at 8:41 AM, Jio M <jiomm.yahoo.com> wrote:
> 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).
>
> regards
> J
>
>
>
>
> On Tuesday, January 14, 2014 3:32 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> 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
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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
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
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> 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)
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Received on Tue Jan 14 2014 - 08:00:03 PST
