On Tue, 2015-06-02 at 17:33 +0100, Angela de Manzanos wrote:
> Dear amber mail list users,
>
> I am simulating a very large multimeric system and I am trying to image
> it in order to study the waters that are in the active sites during the
> simulation. The only way I have successfully managed to obtain a
> reasonable solution using cpptraj V15.01b is by centering first all the
> atoms but the solvent and ions, then imaging the solvent and ions and
> finally do a second centering again of all the atoms relative to the
> center of mass. The commands that I use are as follows:
>
> trajin mysimulation.mdcrd
>
> center !(:WAT,Na+)
>
> image :WAT,Na+ familiar
>
> center mass
Try replacing all of this with the single command "autoimage". It
usually does what you want it to do without any other arguments:
trajin mysimulation.mdcrd
autoimage
trajout autoimage_test.nc netcdf
> trajout autoimage_test.nc netcdf
>
> I know have a question about the imaging step. Am I with this set of
> commands forcing the waters and Na+ in a location different from where
> they are during the simulation? And if not, will this really tell me how
> many waters are close to my ligand during the simulation or I am just
> forcing the waters to be in the periodic box?
Imaging is applicable to simulations employing periodic boundary
conditions. When you're using PBC, each atom has an infinite number of
periodic "images" that you get by simply translating across the unit
cell.
However, when you visualize and analyze, you often need to choose a
single "image" to display and analyze for each atom. The question
becomes "which image should I use?". More often than not, you want the
image with the minimum distance to some other atom (or point in space)
-- the so-called "minimum image convention".
So when you "autoimage" your system, what cpptraj is doing is assigning
each atom in your system to the *image* that is closest to the first
"molecule" (which is centered at the origin). And this is usually what
you want.
Note that some actions automatically invoke the minimum image convention
(unless requested not to) -- like "distance" and "radial".
> I am unsure about how the imaging command works and I am struggling to
> find information about it, so any help on this matter would be very much
> appreciated.
This is a fundamental concept of periodic boundary conditions. There
are many good descriptions of that in various texts (e.g., Allen &
Tildesley, Tuckerman, Cramer, and Leach are ones I'm familiar with).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 02 2015 - 10:00:03 PDT
