molecular-dynamics
Category: chemistry-and-drug-discovery · License: MIT · Version: 1.1
Tags: molecular dynamics, OpenMM, MDAnalysis, simulation, computational chemistry
When to use it
Runs and analyzes molecular dynamics simulations using OpenMM and MDAnalysis. Covers system preparation with PDBFixer and OpenFF/GAFF2, force field choice (AMBER14, CHARMM36m, ff19SB), energy minimization, NVT/NPT equilibration, production MD, and trajectory analysis (RMSD, RMSF, protein-ligand contacts). Use when simulating a protein or protein-ligand system on GPU, assessing how a mutation affects protein dynamics, characterizing ligand binding mode, quantifying per-residue flexibility, or modeling membrane proteins and disordered proteins. Not for GROMACS or NAMD workflows, which the skill lists only as alternatives.Example requests
Ask your agent in plain language, for example:- “I need to run a 100 ns MD of lysozyme on my GPU. Where do I start?”
- “I have 4ake_apo.pdb and a ligand file lig.sdf for a kinase I’m studying. I want to simulate the complex in explicit water with OpenMM, parameterize the ligand with GAFF2 via the OpenFF toolkit, and then compute per-residue RMSF and ligand-protein contacts from the production trajectory in MDAnalysis. Last time I got a ‘No template found for residue’ error from createSystem. How should I set this up?”
- “We found a point mutation in a transporter that patients carry, and we suspect it makes a loop floppier. I have the wild-type structure and want to see whether the mutant moves around more over time compared with wild-type, using atomistic simulation. How would you approach it?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole chemistry-and-drug-discovery category with /plugin install chemistry-and-drug-discovery@research-agent-skills.