I will run amber molecular dynamics simulations with full trajectory analysis

About This Service

Are you working on a protein-ligand system and need reliable, well-analyzed molecular dynamics simulations for your research or publication? I provide end-to-end AMBER MD simulation services from system preparation to publication-ready figures using the same pipeline used in peer-reviewed computational drug discovery research.

I am a computational biology researcher with hands-on experience in AMBER/AmberTools, cpptraj, and Python-based analysis workflows. My work has directly supported manuscripts submitted to peer-reviewed journals in computational pharmacology.

What I Deliver

System Setup

Protein structure preparation and protonation state assignment

Ligand parameterization using antechamber

Solvation (TIP3P or OPC water box), counterion addition

Force field assignment: ff19SB (protein), GAFF2 (small molecule)

Minimization, heating, and NPT/NVT equilibration

Production MD Run

10, 50, or 100 ns production trajectories (package-dependent)

Full .mdcrd trajectory files delivered

Trajectory Analysis (Standard & Premium)

Full publications ready figures

Why Work With Me?

Real amber experience, not a cloud wrapper or online tool.