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I will run gromacs molecular dynamics simulation and analyze your protein
Bioinformatician RNA seq and Single Cell Analysis Bioinformatics Analyst
Hi, I'm Maaz, a biotechnology researcher from Karachi with hands-on experience in bioinformatics. I build reproducible pipelines and turn raw sequencing data into clear results and publication-ready f...
About this Gig
Need a molecular dynamics simulation but stuck on setup, errors, or analysis? I'm a biotechnology researcher with hands-on GROMACS experience, and I'll take your protein from PDB file to publication-ready plots.
What you get:
- Full system preparation (CHARMM36 force field, explicit TIP3P water, ion neutralization)
- Energy minimization, NVT and NPT equilibration, production MD
- Trajectory cleanup (PBC correction, fitting)
- Analysis: RMSD, RMSF, radius of gyration, hydrogen bonds, SASA, secondary structure, and PCA (depending on package)
- Clean, labeled plots (PNG, high resolution) plus the raw data files
- A short methods summary you can adapt for your own report
Please note: I provide the simulation and analysis. Interpretation and write-up of your own research remain yours. Simulation length and system size depend on compute limits, so message me first with your PDB ID or file and I'll confirm feasibility.
Not sure which package fits? Send me a message and I'll recommend one.
My Portfolio
FAQ
What software do you use?
GROMACS, with plots made in Python/Matplotlib and visualization in PyMOL.
How long can the simulation be?
It depends on system size. Message me first and I'll confirm.
Can you simulate membrane proteins?
Not yet. Ask me before ordering. (Only include this if it's true for you. Don't promise membrane systems until you've run one.)
Will you write my thesis section?
No. I provide the simulation, data, figures, and methods summary.
Will I get the input files?
Yes, in the Premium package (or offered as an extra).
