[AMBER] Bugfix 16: New cpptraj action, AutoImage

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 26 Jul 2012 08:36:42 -0600

Hi Amber Community,

Bugfix 16 is currently out for AmberTools12. This bugfix adds a new
command to cpptraj called 'autoimage', the aim of which is to remove a
lot of the guesswork that normally goes into imaging trajectories.
Here is a simple example of the basic usage of this command:

trajin trajectory.nc
autoimage
trajout imaged.nc netcdf

This takes care of centering and imaging, keeping molecules together
that should be together (like DNA strands) and imaging everything else
(like water, ions, etc). If the input molecule has truncated
octahedral boundary conditions, the output molecule will as well (i.e.
'familiar' will be automatically turned on). For most cases
'autoimage' by itself should suffice. For those interested, I will
give a brief explanation of how the algorithm works below, along with
several options that can be used to fine-tune behavior.

If you have any issues (or conversely if autoimage solves imaging
problems for you) let me know!

-Dan

-- 
-------------------------
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) 585-9119 (Fax)
AUTOIMAGE DETAILS:
The algorithm works by grouping molecules into 3 categories: anchor,
mobile, and fixed. The anchor region is a single molecule that
everything will be imaged with respect to. The default is the first
molecule (or molecule specified by 'anchor <mask>'). The mobile region
contains molecules that will be imaged in the standard way; typically
this contains solvent and ions (1 atom "molecules"). Alternatively,
molecules in the mobile region can be specified with 'mobile <mask>'.
The fixed region contains all other molecules (or molecules selected
by 'fixed <mask>'), and these are imaged if and only if the imaging
moves them closer to the anchor.
AUTOIMAGE KEYWORDS:
origin: Center w.r.t. box origin instead of box center.
center: Image molecules in mobile based on molecule center instead of
first atom (molecules in fixed always use center).
familiar: Force truncated octahedral imaging (on if input cell is
truncated octahedral).
triclinic: Force triclinic imaging.
anchor <mask>: Specify anchor molecule (mask MUST specify all atoms of
a single molecule).
fixed <mask>: Specify fixed molecules.
mobile <mask>: Specify mobile molecules.
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Received on Thu Jul 26 2012 - 08:00:03 PDT