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 - 08:00:03 PDT
