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I will run GPU accelerated molecular dynamics simulations for you
Your Computational Biology Expert for All Your Research Needs
Hello and welcome!
I'm a Biotechnology postgraduate with expertise in Computational Biology. My experience spans molecular docking, MD simulations, transcriptomics, biomarker discovery, protein model...
About this Gig
Welcome to my Molecular Dynamics Simulation Gig!
I run GPU-accelerated MD simulations for researchers, students, and biotech teams who need reliable simulation data without access to high-performance computing infrastructure.
What I Offer:
- Full Simulation Pipeline: From raw PDB or SMILES input, I handle system preparation, solvation, ionisation, energy minimisation, NVT/NPT equilibration, and production MD runs.
- Software & Forcefields: GROMACS and AMBER, with CHARMM36m, AMBER ff19SB, GROMOS, and OPLS-AA. Protein, nucleic acid, RNA/protein, membrane, and ligand systems all handled.
- Post-simulation analysis: RMSD, RMSF, Rg, H-bonds, PCA, MM/PBSA, MM/GBSA, and more depending on your package.
- Publication-Ready Figures: High-resolution plots and molecular visualisations using PyMOL, VMD, and R/ggplot2.
- Custom Add-ons: Coarse-grained (CG) simulations and QM/MM analysis (ORCA-GROMACS) available on request.
Message me before ordering if you have a large system or specific simulation requirements. I am happy to collaborate. Let's work together to move your research forward!
FAQ
What input files do I need to provide?
A protein structure file (PDB or mmCIF) and, if applicable, your ligand in SDF, MOL2, or SMILES format. If you only have a UniProt ID or PDB code, I can fetch and prepare the structure myself.
Which software and forcefields do you use?
GROMACS and AMBER. Forcefields: CHARMM36m, AMBER ff19SB, GROMOS96, and OPLS-AA. Water models: TIP3P and SPC/E. If you have a specific requirement, mention it before ordering.
What system types can you simulate?
Protein-ligand, protein-protein, RNA/DNA-protein complexes, membrane proteins, and standalone nucleic acid systems. For unusual systems, message me first to confirm feasibility.
How long will my simulation take?
Depends on system size and simulation length. A 100ns run typically delivers in 2-3 days, 300ns in 4-5 days, and 500ns+ in 7 days.
What computing infrastructure do you use for simulations?
I run simulations on high-performance GPU servers, including RTX 4090 and RTX 5090 nodes. On a 5090, a 100k+ atom system runs at approximately 250-300ns/day, ensuring fast turnaround without compromising simulation quality.
Can you perform coarse-grained or QM/MM simulations?
Yes, both are available as custom add-ons. CG simulations use the MARTINI force field. QM/MM is run via ORCA coupled with GROMACS. Message me to discuss scope and pricing before ordering.
Is my data confidential?
Yes. I do not share client structures, sequences, or results with anyone, and I am happy to sign an NDA if required.
