On Tue, 2014-03-11 at 06:37 +0000, Vijay Manickam Achari wrote:
> Dear Dan, Jason, and David,
>
> Thanks for your prompt response. Well, I keep trying those commands
> that you suggested but I don't get of what I want. I keep seeing the
> layers of water like climbing a ladder. The same goes to those lipids
> layers as well.
>
> As to understand what is going on during the processing of the
> trajectories, I would like to investigate these commands one bye one
> systematically.
>
> Start from first I tried to use the command
>
> ptraj topology.top << EOF
> trajin abcdef01.traj
> trajin abcdef012traj
> ..
> ..
> ..
> unwrap :1-1214
>
> trajout ABCD.nc netcdf
> EOF
>
> I notice some of the water molecules become so big in size compare to
> the other water molecules. I have attached a snapshot of that for your
> view. It is really surprising me. Why few water molecules having some
> length bonds?
Are you using "orthographic" or "perspective" view in VMD? If the
latter, then the "big" water molecules are just the ones that are closer
to you. If you rotate the system, the "big" molecules will move
backwards in the screen and appear smaller (but ones that have rotated
to the front will now appear much larger).
Also note that trajectories are stored in single precision in NetCDF
format. Therefore, as the coordinates get larger (i.e., as waters
diffuse farther and farther away), these numbers begin to lose precision
and you may see strange artifacts as a result.
In the end, the _only_ reason that I can think of that you would want to
"unwrap" your trajectory would be in order to study diffusion properties
(and even then you need to run in the NVE ensemble to get meaningful
results, I believe).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 11 2014 - 05:00:03 PDT
