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ReactorMD Computational Service

Molecular dynamics trajectory analysis for runs you already have

Already finished a simulation? Send the trajectory and topology. ReactorMD corrects periodic boundaries, runs the standard analysis suite and writes up what the plots mean for your system.

Who this service is for

  • Researchers who ran MD themselves but need analysis and figures
  • Students who need help interpreting RMSD and RMSF
  • Groups wanting publication-style plots

What to send us

  • Trajectory (XTC or TRR) and matching topology or structure (TPR, GRO)
  • Index groups or residues of interest
  • The questions you want answered

How the work is done

  1. Check the files and fix periodic boundary effects and centring.
  2. Fit the trajectory and select analysis groups.
  3. Compute RMSD, RMSF, radius of gyration, SASA and hydrogen bonds.
  4. Run contact, PCA, clustering and free-energy landscape analysis when relevant.
  5. Create figures and write a short interpretation.

What you receive

  • Plots and the underlying data files
  • Short interpretation of stability, flexibility and interactions
  • Scripts or commands used, for reproducibility

What this method can and cannot tell you

Analysis can only describe what the simulation sampled. If the run is short, not converged or poorly equilibrated, the report says so.

Frequently asked questions

Which trajectory formats do you accept?

GROMACS XTC or TRR with TPR or GRO topology. Other formats can be handled on request.

Can you analyse a simulation not run with GROMACS?

Often yes, if it can be converted. Contact ReactorMD with the engine and file types.

Do you help interpret the plots?

Yes. The report explains what each plot shows for your system and flags limitations.

Is this the same as the analysis in the MD service?

The MD service already includes this analysis. This service is for trajectories you generated elsewhere.

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Computational results are predictions and support, but do not replace, experimental validation. Page reviewed by ReactorMD, 16 October 2026.