GROMACS trajectory and polymer-interface analysis

Legacy Fortran and shell tools for post-processing molecular-dynamics trajectories, with emphasis on polymer exposure at liquid interfaces.

Functions and engineering applications

Source	Observed function / inputs and outputs	Inferred engineering application
AnalyzeGro4annotated.f	Reads concatenated GRO frames from md.gro and a residue label from standard input; classifies target atoms as exposed above/below overlapping atoms and writes five ratios to r.dat	Comparing polymer surface exposure across cosolvent compositions [1]
Downstream_TRJCONV.sh, Downstream_TRJCONV_DensityCalcu.sh	Trajectory conversion and density-analysis commands	Preparing interfacial density profiles
Downstream_MultipleCalculations.sh, Downstream_MultipleCalculations2.sh	Calls legacy GROMACS tools for RDF, density, MSD, gyration, and energy	Comparing solvation, mobility, chain dimensions, and equilibration [2]
Downstream_Hbond.sh, Downstream_GEnergyComputations.sh	Hydrogen-bond and energy extraction wrappers	Relating association and energetic changes to composition

These applications are interpretations of the code, not demonstrated performance claims. Atom exposure is not directly a surface tension, adsorption free energy, or solvent-accessible surface area.

Example calls

Prerequisites: a fixed-form Fortran compiler, a compatible GROMACS environment, and simulation files generated separately. Build from source rather than relying on the archived executables:

gfortran -std=legacy -ffixed-line-length-none -fcheck=all \
  'AnalyzeGro4annotated.f' -o analyze_gro
# In a working directory containing md.gro, run interactively:
./analyze_gro

Enter the exact target residue identifier when prompted. The inspected source expects 10 frames, at most 22,000 atoms, and a four-character residue field. Adjust these source assumptions for other datasets before compilation. Output columns are cumulative maximum-side/total, cumulative top/total, cumulative bottom/total, current top/total, and current bottom/total.

For a legacy GROMACS 4.x installation, representative calls extracted from the workflow are:

g_density -f md_concat.trr -s md1.tpr -o density_z.xvg -dens mass -symm -d Z
g_msd -f md_concat.trr -s md1.tpr -o msd.xvg

Choose the intended molecular group interactively. The named inputs are external prerequisites. These calls were checked against the scripts but were not executed with trajectories in this review.

Reproducibility and limitations

The scripts contain historical absolute paths, module names, numeric group selections, and ambiguous shell expansions such as $XOH; adapt these explicitly. Modern GROMACS CLI names and options differ. GRO coordinates normally use nm, while the Fortran radii include values such as 1.52 and 1.70 without conversion: resolve the unit convention before interpreting exposure ratios. The code applies x/y periodic images, modifies some z coordinates, and can divide by zero if the target is absent. Validate against hand-constructed frames, not only smooth-looking plots. No trajectory data or end-to-end reproduction is supplied here.

Review scope and software citation

Documentation reviewed on 2026-10-08 against source commit 382760ba805f. “Observed” means supported by source inspection; engineering applications are reasoned possibilities unless explicitly demonstrated. Scholarly references provide methodological context and do not certify these implementations. Runtime validation is stated separately above.

For software attribution, cite Guy Francis Mongelli, GromacsAnalyses, the repository, the exact commit used, and your access date. Also cite the relevant method publications and any original third-party contributors. No unverified software DOI or release version is assigned by this documentation.

Scholarly references

1. “The surface activity of polymers in cosolvated systems determined from computational simulation.” Polymer (2016). DOI: 10.1016/j.polymer.2015.11.003. Related polymer/cosolvent surface-activity research. The publisher indexes the journal publication as 2016; the DOI contains 2015. Exact reproduction requires the original inputs and analysis conventions.

2. M. J. Abraham et al. (2015). “GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.” SoftwareX 1–2, 19–25. DOI: 10.1016/j.softx.2015.06.001. Background for the simulation and analysis ecosystem; this does not establish compatibility with the legacy scripts.

Ownership and existing license notices

Copyright (c) 2025 Guy Francis Mongelli

The existing project notice declares Apache License 2.0 for project code. Documentation, prose, and figures are declared CC BY 4.0; notebook code cells are Apache-2.0 and narrative/figures CC BY 4.0. Preserve all file-level and third-party notices. This README update does not change ownership or licensing terms.

Reproducibility, source verification, and contribution policy (2026-10-08)

• Observed versus proposed: The function inventory above describes inspected source where indicated. Engineering applications identified as inferred are potential uses, not verified features or validated performance claims.
• Usage examples: Treat the documented commands and calls as illustrative until the referenced source file, runtime version, dependencies, required input data, and working directory have been checked. Do not execute notebook fragments or batch-scheduler directives as standalone programs without adapting their context.
• Scientific citations: References above identify relevant governing methods and computational background; citing a publication does not imply that its algorithm is implemented in this repository or that the publication was authored by this repository owner.
• Missing or null artifacts: Empty, placeholder, missing, or non-executable source files must not be represented as functional implementations. Candidate restorations from personal archives require provenance, content comparison, license review, and explicit verification before committing code.
• Access model: This repository is publicly readable. Public visibility does not grant anonymous push rights; write access is controlled separately through repository collaborators, credentials, apps, deploy keys, and branch rules. This README is descriptive and does not itself enforce permissions.