Thank you Daniel for your feedback!
~Kenneth
Kenneth N. McGuinness Ph.D
Research Associate
Advanced Science Research Center CUNY
Adviser: Dr. Rein Ulijn <http://www.ulijnlab.com/>
Cell: 928-925-7693
On Mon, May 2, 2016 at 10:40 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Mon, May 2, 2016 at 7:53 AM, Kenneth McGuinness
> <kenneth.mcguinness.gmail.com> wrote:
> >
> > trajin 'simulationFileName.crd' 1 -1 1
> > unwrap !(:WAT)
> > center mass origin !(:WAT)
> > autoimage origin familiar
> > rams first mass !(:WAT)
> > trajout 'correctedTrajFileName.crd'
>
> Just a couple of notes on this cpptraj input:
>
> 1) The 'unwrap' and 'center' commands are unnecessary - they are
> effectively wiped out by the subsequent 'autoimage' command.
>
> 2) I think you meant 'rms', not 'rams'
>
> 3) Be aware that the rotations that occur during the RMS best-fit (the
> 'rms' command) means you will no longer be able to perform any imaging
> on that trajectory. If you need imaging, make sure you don't rms
> best-fit. If you don't, you may as well get rid of the box coordinates
> in the output trajectory (i.e. use the 'nobox' keyword for 'trajout').
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> 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 Mon May 02 2016 - 08:30:04 PDT
