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I will run any gromacs molecular dynamics simulation and trajectory analysis
Embark on a journey of creativity and precision with Experts
I'm Jalal Khan Utman, an MS Biotechnology researcher (PAF-IAST) who works on both sides of the bench: computational drug discovery (AutoDock Vina, GROMACS with CHARMM36m, PyMOL, Linux/SLURM HPC) and w...
About this Gig
Need publication-grade Molecular Dynamics (MD) simulations in GROMACS? I set up, run, and analyze biomolecular systems using GPU-accelerated HPC clusters.
SYSTEMS COVERED:
- Protein-Ligand complexes (small molecules, natural compounds)
- Apo-proteins & Wild-type vs. Mutant comparative stability
- Protein-Protein and Peptide-Receptor complexes
- Membrane proteins (lipid bilayer insertion & solvation)
- Nanoparticle-biomolecule interactions
WORKFLOW & FORCE FIELDS:
- Parameterization via CHARMM36m/CGenFF, AMBER/GAFF2, and OPLS-AA
- GPU-accelerated production runs managed via Linux/SLURM environments
- Solvation, neutralization, minimization, NVT/NPT equilibration
TRAJECTORY ANALYSIS & DELIVERABLES:
- Structural metrics: RMSD, RMSF, Radius of Gyration (Rg), and SASA
- Interaction dynamics: Hydrogen bonds, contact maps, and PCA
- Deliverables: Coordinate (.gro/.pdb), clean trajectory (.xtc), raw .xvg files, publication vector plots (300 DPI), and methods write-up.
Please message me with your PDB ID, system details, and simulation length before ordering!
Technology:
Other
Expertise:
Experiment design
•
Algorithms
•
Monte Carlo simulation
Programming language:
Python
•
Other
My Portfolio
FAQ
Can you simulate systems other than protein-ligand?
Yes. I handle apo-proteins, point mutations, protein-peptide complexes, lipid membrane embeddings, and nanoparticle-protein interfaces.
What hardware do you use for production runs?
Simulations are executed on high-performance GPU nodes using SLURM job scheduling and containerized environments for fast turnaround.
Do you provide the trajectory files?
Yes, you receive all topology, parameter (.mdp), coordinate, and processed trajectory files alongside high-resolution figures.
