Upload Portal: Simulation files from Franci Merzel

[simulation-addition-helper]

This PR contains simulation files uploaded by @fmrz through the NMRlipids upload portal.

Processing of simulation data will happen after approval.

[MagnusSletten]

Negative frame calculation? @comcon1

10:41:13 AM [INFO]: Starting parallel trajectory centering: -2045481502 frames, 4 workers, ~-511370375 frames/chunk
10:41:13 AM [INFO]: Dispatching 0 chunks for parallel processing
10:41:13 AM [INFO]: Merging trajectory chunks...
10:41:13 AM [INFO]: Parallel centering complete: /__w/BilayerData/BilayerData/BilayerData/Simulations/f77/d85/f77d85ddda6a649bc8d5dbea0ba00035cf138a16/f77d85ddda6a649bc8d5dbea0ba00035cf138a16/whole.xtc
10:41:13 AM [ERROR]: Calculation MAICOS failed for f77/d85/f77d85ddda6a649bc8d5dbea0ba00035cf138a16/f77d85ddda6a649bc8d5dbea0ba00035cf138a16.
Traceback (most recent call last):
...
OSError: XDR read error = endoffile

[comcon1]

Negative frame calculation? @comcon1

10:41:13 AM [INFO]: Starting parallel trajectory centering: -2045481502 frames, 4 workers, ~-511370375 frames/chunk
10:41:13 AM [INFO]: Dispatching 0 chunks for parallel processing
10:41:13 AM [INFO]: Merging trajectory chunks...
10:41:13 AM [INFO]: Parallel centering complete: /__w/BilayerData/BilayerData/BilayerData/Simulations/f77/d85/f77d85ddda6a649bc8d5dbea0ba00035cf138a16/f77d85ddda6a649bc8d5dbea0ba00035cf138a16/whole.xtc
10:41:13 AM [ERROR]: Calculation MAICOS failed for f77/d85/f77d85ddda6a649bc8d5dbea0ba00035cf138a16/f77d85ddda6a649bc8d5dbea0ba00035cf138a16.
Traceback (most recent call last):
...
OSError: XDR read error = endoffile

This have to be debugged locally. I don't see the easy way to understand this report.

[comcon1]

Dear @frmz! Thank you again for your contribution. Your trajectory is not time-aware. We can guess what is the time interval btw frames, but it doesn't seem to be written anywhere. MDAnalysis (I tried both 2.9 and 2.10) doesn't see time btw frames. It sets it by default to something like 0.0048fs which is nonsence. It's likely many ps. Can you, please, enrich your DCD with proper DELTA header and update the file on Zenodo. AI recommends me the following solution:

#!/usr/bin/env python3

import sys
import MDAnalysis as mda
from MDAnalysis.coordinates.DCD import DCDWriter

if len(sys.argv) != 3:
    print(f"Usage: {sys.argv[0]} input.dcd output.dcd")
    sys.exit(1)

input_dcd = sys.argv[1]
output_dcd = sys.argv[2]

FRAME_DT_PS = 200.0
NSAVC = 100000
FIRST_TIMESTEP = 0

u = mda.Universe(input_dcd)

with DCDWriter(
    output_dcd,
    n_atoms=u.atoms.n_atoms,
    dt=FRAME_DT_PS,
    nsavc=NSAVC,
    istart=FIRST_TIMESTEP,
) as w:
    for i, ts in enumerate(u.trajectory):
        ts.time = i * FRAME_DT_PS
        w.write(u.atoms)

print(f"Created {output_dcd}")
print(f"Frames : {len(u.trajectory)}")
print(f"Atoms  : {u.atoms.n_atoms}")
print(f"dt     : {FRAME_DT_PS} ps")
print(f"NSAVC  : {NSAVC}")

If it works, we will include it in the instructions on system uploading for be egligible for processing.

It's not only our project's wish. If you want to make your trajectory interoperable (i.e., to satisfy F.A.I.R. principles), you should have this information in some machine-readable form. It is one of the ways to do it.