openmm-system-minimization

Name: openmm-system-minimization
Author: ma-compbio-lab

36stars5forks

How to install openmm-system-minimization?

ma-compbio-lab/skillfoundry/openmm-system-minimization

$npx -y skills add ma-compbio-lab/SkillFoundry --skill openmm-system-minimization

Installs into the current project.

Summary

Use this skill to run a deterministic OpenMM energy minimization on a tiny toy system. Do not use it for production molecular dynamics or force-field validation.

Files · 1

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SKILL.md

1	## Purpose
2	Provide a minimal, runnable OpenMM starter that creates a small bonded system, minimizes its energy, and reports before/after energies and coordinates.
3
4	## When to use
5	- You need a verified local OpenMM entry point.
6	- You want a tiny deterministic minimization example before scaling to larger simulations.
7
8	## When not to use
9	- You need biomolecular force-field preparation or explicit-solvent production runs.
10	- You need ensemble sampling or long-timescale trajectories.
11
12	## Inputs
13	- Optional JSON summary path
14
15	## Outputs
16	- JSON summary with OpenMM version, platform, initial/final potential energy, and final coordinates
17
18	## Requirements
19	- `slurm/envs/chem-tools` with OpenMM available
20
21	## Procedure
22	1. Run `slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/openmm-system-minimization/scripts/run_openmm_minimization.py`.
23	2. Compare `initial_potential_energy_kj_mol` and `final_potential_energy_kj_mol`.
24	3. Reuse the script as a seed for more realistic system-building workflows.
25
26	## Validation
27	- The command exits successfully.
28	- Final potential energy is lower than the initial potential energy.
29	- Final coordinates are emitted for all particles.
30
31	## Failure modes and fixes
32	- Missing OpenMM environment: run the script with `slurm/envs/chem-tools/bin/python`.
33	- Numerical issues: reset the toy system to the bundled defaults.
34
35	## Safety and limits
36	- Educational starter only.
37	- This is not a physically meaningful production system.
38
39	## Provenance
40	- OpenMM user guide: https://docs.openmm.org/latest/userguide/
41
42	## Related skills
43	- `rdkit-molecular-descriptors`

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openmm-system-minimization

36stars5forks

View on GitHub

How to install openmm-system-minimization?

ma-compbio-lab/skillfoundry/openmm-system-minimization

$npx -y skills add ma-compbio-lab/SkillFoundry --skill openmm-system-minimization

Installs into the current project.

Summary

Use this skill to run a deterministic OpenMM energy minimization on a tiny toy system. Do not use it for production molecular dynamics or force-field validation.

Files · 1

View on GitHub

SKILL.md

1	## Purpose
2	Provide a minimal, runnable OpenMM starter that creates a small bonded system, minimizes its energy, and reports before/after energies and coordinates.
3
4	## When to use
5	- You need a verified local OpenMM entry point.
6	- You want a tiny deterministic minimization example before scaling to larger simulations.
7
8	## When not to use
9	- You need biomolecular force-field preparation or explicit-solvent production runs.
10	- You need ensemble sampling or long-timescale trajectories.
11
12	## Inputs
13	- Optional JSON summary path
14
15	## Outputs
16	- JSON summary with OpenMM version, platform, initial/final potential energy, and final coordinates
17
18	## Requirements
19	- `slurm/envs/chem-tools` with OpenMM available
20
21	## Procedure
22	1. Run `slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/openmm-system-minimization/scripts/run_openmm_minimization.py`.
23	2. Compare `initial_potential_energy_kj_mol` and `final_potential_energy_kj_mol`.
24	3. Reuse the script as a seed for more realistic system-building workflows.
25
26	## Validation
27	- The command exits successfully.
28	- Final potential energy is lower than the initial potential energy.
29	- Final coordinates are emitted for all particles.
30
31	## Failure modes and fixes
32	- Missing OpenMM environment: run the script with `slurm/envs/chem-tools/bin/python`.
33	- Numerical issues: reset the toy system to the bundled defaults.
34
35	## Safety and limits
36	- Educational starter only.
37	- This is not a physically meaningful production system.
38
39	## Provenance
40	- OpenMM user guide: https://docs.openmm.org/latest/userguide/
41
42	## Related skills
43	- `rdkit-molecular-descriptors`

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6 picks

Type