Hi,
This warning occurs after you have performed a rotation on your
coordinates (via e.g. an RMS best-fit). This also rotates your unit
cell so that it is no longer X-aligned, hence the warning. Note that
this has *always* been an issue, it's just that cpptraj is much better
about reporting it now.
What does it mean to be X-aligned? It just means that your unit cell A
B and C vectors are related to the Cartesian X Y and Z axes in a very
specific way: the A vector is aligned along the X axis (hence
"X-aligned"), and the B vector is in the X-Y plane. The advantage of
using an X-aligned unit cell is that it allows a reduced
representation of the unit cell vectors. Normally you need 9
coordinates, 3 coordinates per unit cell vector (Ax Ay Az Bx By Bz Cx
Cy Cz), but when you are X-aligned the Ay, Az, and Bz components are
all zero, meaning you can represent the unit cell with only 6
coordinates (either Ax Bx By Cx Cy Cz or 3x lengths and 3x angles).
Lots of MD packages use this representation.
However, when you rotate your unit cell you are no longer X-aligned,
and the Ay Az and Bz components are no longer zero, so you now need
all 9 unit cell coordinates. Unfortunately many MD trajectory formats
are not set up to support this (it's on my to-do list for NetCDF); the
current exceptions are the Gromacs trajectory formats (TRR, XTC) which
store all 9 unit cell vector coordinates.
So if you don't care about the rotated unit cell you can either remove
the box information or ignore the warnings, but be aware you won't be
able to perform imaging for those coordinates. Or you can write using
the TRR format. As I said, NetCDF support is on my to-do
list...hopefully soon.
Hope this helps,
-Dan
On Mon, Aug 9, 2021 at 9:38 PM 刘保艳 <870726grin.163.com> wrote:
>
> Dear All,
> I met warnings as follows when I try to use cpptraj to analyze netcdf files for every frame:
>
>
> Warning: Set 4998; unit cell is not X-aligned. Box cannot be properly stored as Amber NetCDF trajectory.
> Warning: Set 4999; unit cell is not X-aligned. Box cannot be properly stored as Amber NetCDF trajectory.
> Warning: Set 5000; unit cell is not X-aligned. Box cannot be properly stored as Amber NetCDF trajectory.
> 100% Complete.
>
>
> Anyone can give me some advice? Thank you all.
>
>
>
>
> all the best,
> Liu
>
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Received on Wed Aug 11 2021 - 07:00:02 PDT
