Hi,
Under periodic boundary conditions it doesn't matter where a
particular molecule appears to be since there are effectively
infinitely repeating unit cells along each box vector. However, for
visualization purposes or for certain actions (such as calculating a
best-fit RMSD) it may be necessary to re-image the trajectory so that
a molecule of interest appears to be at the center of the primary
cell. For example, say you have a protein-ligand system which is right
near a cell boundary and you have coordinate wrapping turned on
(iwrap=1). The protein may appear to "jump" from one side of the cell
to the other (or vice versa) making it "look" like the system has
dissociated. This has no effect on the simulation because of the
periodic boundary conditions (they are still interacting across the
unit cell boundary) and is simply a visualization artifact; however if
you were to for example perform an RMSD calculation of the complex the
resulting RMS value would seem to suddenly "jump". The cpptraj action
'autoimage' was designed specifically to make this re-imaging easy.
On Tue, Jul 9, 2013 at 8:07 PM, Parker de Waal <Parker.deWaal09.kzoo.edu> wrote:
> From my knowledge it seems that re-imaging a trajectory, after a simulation
> has been run, removes excess waters that have moved out of the original box
> coordinates.
Not exactly. Imaging wraps molecules that have moved outside the
primary cell back into the primary cell. So again, if your molecule is
right near a unit cell boundary and you shift all of your coordinates
so that molecule is now at the center of the unit cell, some molecules
will now be outside the box and need to be "wrapped" back in. I will
try to illustrate with bad ASCII art (it looks way better in fixed
width font).
Original Cell; 'X' and 'o' are molecules:
_______
| |
| X o|
| |
-------
Centered on 'X'; 'o' is now shifted out of the primary cell:
_______
| |
| X |o
| |
-------
'o' is wrapped (imaged) back into the primary cell.
_______
| |
|o X |
| |
-------
> In terms of NVE simulations would it be advantageous to run a
> short 1-2 ns simulation, re-image the trajectory, and then use the new
> trajectory coordinates to continue with a full 20 ns NVE simulation?
As far as I know re-imaging the trajectory should have no affect on
the dynamics. The one exception is possibly if you have distance
restraints, which I think are not imaged.
Hope this helps,
-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)
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Received on Tue Jul 09 2013 - 20:00:02 PDT
