On Wed, Sep 2, 2015 at 4:21 PM, Eg eh <egeh00.yahoo.com> wrote:
> Dear all,
> I am using CPPTRAJ to calculate diffusion and mask. I found the results
> were different if I added "autoimage" in the script. I did not set iwrap in
> my MD input file. If I used VMD to check the trajectory file, I got an
> almost spherical water box.
There's no such thing as a spherical box. Certain shapes can have more
spherical symmetry than others (for example, the truncated octahedron is
more spherical than the orthorhombic cell in Amber, and a dodecahedron is
even moreso). If you have iwrap=0, then particles can diffuse *out* of
their "current" unit cell and into adjacent ones. If you allow a
simulation to go on long enough, you may get what appears to be a spherical
distribution of atoms around the central unit cell. But that is purely a
visualization artifact.
Look at the angles between your unit cell vectors (the last line of the
inpcrd file). If they are 90 degrees, then you have an orthorhombic cell
(what you call 'cubic').
> If I "autoimage" the trajectory file, I got a cubic waterbox. Which way is
> right for the calculation?
They are equivalent representations under periodic boundary conditions.
If you are studying diffusion, however, you typically need an unimaged
trajectory, not an imaged one. Any calculation that explicitly accounts
for the minimum image convention is completely unaffected by your choice of
representation here.
> I am really confused about how CPPTRAJ calculated for a PBC water box.
>
cpptraj does not calculate the PBCs. The PBCs are defined for each frame
of the trajectory. Many actions use the PBCs to compute minimum image
distances (the documentation usually says when this is true).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 02 2015 - 14:00:03 PDT
