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Can trajectory files, such as MD_dump, be converted to the .xyz format? #5022

@qinrui-oss

Description

@qinrui-oss

Background

After running a Molecular Dynamics (MD) simulation, it is often necessary to parse the output files to calculate the Mean Square Displacement (MSD). The output file, MD_dump, contains essential information such as time, position, and velocity. However, most post-processing tools, such as VMD, GROMACS, and Python MDAnalysis, cannot directly read the MD_dump file, which makes further analysis inconvenient.

Describe the solution you'd like

It would be more convenient if the trajectory file could be generated in the .xyz format after the MD simulation. The .xyz file can be read by VMD and Python MDAnalysis, and it can be converted to the g96 format using ASE. This g96 format can then be further converted to the trr format using GROMACS for calculating the MSD.

Task list only for developers

  • Notice possible changes of behavior
  • Explain the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi

Notice Possible Changes of Behavior (Reminder only for developers)

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Notice any changes of core modules (Reminder only for developers)

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Task list for Issue attackers (only for developers)

  • Review and understand the proposed feature and its importance.
  • Research on the existing solutions and relevant research articles/resources.
  • Discuss with the team to evaluate the feasibility of implementing the feature.
  • Create a design document outlining the proposed solution and implementation details.
  • Get feedback from the team on the design document.
  • Develop the feature following the agreed design.
  • Write unit tests and integration tests for the feature.
  • Update the documentation to include the new feature.
  • Perform code review and address any issues.
  • Merge the feature into the main branch.
  • Monitor for any issues or bugs reported by users after the feature is released.
  • Address any issues or bugs reported by users and continuously improve the feature.

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Input&OutputSuitable for coders without knowing too many DFT detailsMD & LAMMD and Larege Atomic Models

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