Hello
Thank you so much for your reply.
By random rotation, I mean the rotation that I observed happens too quick to
be true. In my opinion, the time scale of the rotation should be around 1 ns
or more. But the rotation in my case just happen within a couple of 100 fs.
Please check the animation from links in my very first mail.
That is why I believe, those rotation might be artificial resulted from PBC
and imaging issues.
And I have tried with rms command prior and after the image commands. Still
no luck.
Any suggestions?
Thank you very much.
Bin
2011/8/24 Thomas Cheatham III <tec3.utah.edu>
>
> > trajin traj.mdcrd 1 1000000 20
> > center :1-125 mass origin
> > image origin center familiar
> > trajout traj_reimage.mdcrd
> > go
> >
> > I also tried to use "rms first :1-125" and/or "unwrap :1-125" within the
> > above script. (right before the "center" line)
>
> You cannot do the rms command prior to imaging since this will rotate the
> box and break the imaging process (since the box frame of reference is not
> rotated).
>
> Molecules do rotate naturally. If you want to see a movie or trajectory
> without this rotation, you center/image first, and then do the RMS fit
> with the RMS command. The box will rotate with the molecule.
>
> --tec3
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 24 2011 - 16:00:02 PDT
