A historical collection of shell/PBS scripts for preparing, submitting, continuing, and analyzing GROMACS simulations of polymers in mixed solvents. Several files are planning drafts rather than executable workflows.
| Files | Observed purpose | Inferred use |
|---|---|---|
1_pregrompp.pbs, 2_mixing.pbs, 3_mdgrompp.pbs |
Preparation/mixing/preprocessing stages, with incomplete preparation logic | Organizing composition and polymer-size studies [1,2] |
md.pbs, md2.pbs, secondmd.pbs, thirdmd.pbs |
PBS resource requests and MPI molecular-dynamics runs | Long-running simulation campaigns |
sequentialMDRuns.sh, sequentialMDRuns2.sh, sequentialMDAll2A.sh |
Sequential job/continuation workflows | Chaining production segments with scheduler adaptation |
RDF_MSDComputations.pbs, DensityComputations.pbs, GEnergyComputations.pbs, AnalyzeGroALL.pbs |
Analysis wrappers; the inspected RDF/MSD-named file actually invokes RDF commands | Solvation, density, energetics, and interface comparisons [1,2] |
CreatingBackupTARFiles.pbs, copying*.pbs, FindAndReplace*.sh |
Archiving, staging, and template editing | Managing reproducible simulation inputs and outputs |
Lumerical_8.pbs |
Separate Lumerical batch-job template | Historical optical-simulation scheduling, not a GROMACS analysis step |
Requires Bash, a PBS-compatible scheduler, site-specific modules/MPI, and the GROMACS/input versions expected by each script. PACKMOL is relevant to preparation [3], but its input structures are not bundled as a complete runnable system.
# Syntax checks do not submit jobs or run simulations.
bash -n md.pbs
bash -n RDF_MSDComputations.pbsAfter editing the PBS resources, paths, module names, output destinations, and input filenames for your cluster, a single-job submission follows this interface:
qsub md.pbsThis is a scheduler invocation example, not confirmation that the unmodified template runs on your cluster. Review the selected file before submission. Use individual jobs before enabling the mass-submission scripts.
1_pregrompp.pbs contains unfinished constructs such as if k=1, s= and malformed loop headers. It must be completed before use. Other scripts embed historical user paths, email directives, and module versions. Source filenames alone do not establish capability: inspect actual commands and expected outputs. Backup/copy/replacement scripts modify files in place and must be adapted to a working copy. Expected artifacts depend on the job: trajectories (.trr), energies (.edr), logs, structures, or analysis (.xvg/.dat). No scheduler jobs were submitted during this documentation review. Validate one small complete case and checkpoint continuation before expanding a sweep.
Documentation reviewed on 2026-10-08 against source commit 13f8fddb8699. “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, BashScriptsForMassSimulations, 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.
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“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.
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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.
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L. Martínez, R. Andrade, E. G. Birgin, and J. M. Martínez (2009). “PACKMOL: A package for building initial configurations for molecular dynamics simulations.” Journal of Computational Chemistry 30, 2157–2164. DOI: 10.1002/jcc.21224. Supports molecular packing and initialization workflows.
Copyright (c) 2025 Guy Francis Mongelli
The existing project notice declares Apache License 2.0 for project code. Preserve all file-level and third-party notices. This README update does not change ownership or licensing terms.
- 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.