yes that's the warning message that I mentioned. It is telling you that you
won't be able to calculate periodic system energies for the output
coordinates. Imaging involves wrapping molecules across the boundary, but
does not fix a rotated cell.
On Tue, May 27, 2025 at 12:50 PM Helmut Carter <hcarter.gradcenter.cuny.edu>
wrote:
> Thank you for your reply! During output, I get the following
> warnings/errors:
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly stored
> as Amber NetCDF trajectory.
> Error: Unit cell is not X-aligned or symmetric; cannot set PME recip grid.
> Warning: aligned.nc: unit cell was not X-aligned for 2 frames.
> Warning: This trajectory format expects unit cells to be X-aligned,
> Warning: so the unit cell orientation may not be correct.
>
> If the issue is based on the system being outside the periodic cell, I
> would (perhaps naively) expect autoimaging to fix this issue but it doesn't
> in my experience. Also, crucially, the energies are correct after
> alignment, but incorrect after saving and loading the aligned trajectory.
>
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Tuesday, May 27, 2025 12:38 PM
> *To:* Helmut Carter <hcarter.gradcenter.cuny.edu>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* [EXTERNAL]Re: [AMBER] Bug in CPPTRAJ following alignment
>
> ****ATTENTION:* This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected emails.***
> I don't know the details of your system, but aligning a trajectory carried
> out in a periodic system can shift it such that the system no longer fits
> in the periodic cell that was originally present. the resulting energies
> will indeed be far off, since the system does not fit in a periodic cell
> but you are asking Amber to calculate the energies using that cell.
> In my experience cpptraj warns about this when it processes that command.
> Did you see anything in the output when you did the trajout step?
>
> On Tue, May 27, 2025 at 12:34 PM Helmut Carter via AMBER <
> amber.ambermd.org> wrote:
>
> Hello,
>
> I have found a bug in CPPTRAJ where aligning a trajectory, saving it, then
> loading it causes incorrect energies, possibly due to the placement of
> non-target atoms (that is, atoms in the mask for align). In a minimal
> example using a small molecule solvated in water, where the trajectory is 2
> frames, the following happens:
> # script 1
> parm example.parm7
> trajin example.nc
> <https://urldefense.com/v3/__http://example.nc__;!!GIqKXF0_-xZi!qrma9POWUHL7SvcAAgX6ewfhi09B3FyP7BhuR8AVCK3au-hCUfSXC1lEUoe1Kpr0s20IlKcuneUhT2ZHd3iDEcrnP0n6grtHWUE$>
> align !(:WAT)
> trajout aligned.nc
> <https://urldefense.com/v3/__http://aligned.nc__;!!GIqKXF0_-xZi!qrma9POWUHL7SvcAAgX6ewfhi09B3FyP7BhuR8AVCK3au-hCUfSXC1lEUoe1Kpr0s20IlKcuneUhT2ZHd3iDEcrnP0n6tpsFO-g$>
> energy * etype pme cut 9
> go
> avg(ENE_00001[total]) # returns -17959.450391 as expected
> check
> go # no warnings from check
>
> # script 2
> parm example.parm7
> trajin aligned.nc
> <https://urldefense.com/v3/__http://aligned.nc__;!!GIqKXF0_-xZi!qrma9POWUHL7SvcAAgX6ewfhi09B3FyP7BhuR8AVCK3au-hCUfSXC1lEUoe1Kpr0s20IlKcuneUhT2ZHd3iDEcrnP0n6tpsFO-g$>
> energy * etype pme cut 9
> go
> avg(ENE_00001[total]) # returns 84244.631388
> check
> go # 10 close contact warnings from check
>
> By varying the energy mask, I have found that the incorrect energy stems
> from the solvent molecules. In the analysis of a 5 frame long trajectory,
> the energy after saving and loading was 35591055618150936.000000. This bug
> happens with V6.4.4 from AmberTools and V6.29.13 from GitHub. Please let me
> know if there's any more useful information I can provide.
>
> Thank you,
> Helmut Carter
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>
>
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Received on Tue May 27 2025 - 10:00:04 PDT
