Which MD analyses can you include?

Common outputs include RMSD, RMSF, SASA, radius of gyration, hydrogen bonds, distance analysis, contact maps, PCA, and free energy landscape when suitable.

Can you follow a journal-specific method?

Yes. Share the target paper or journal requirement, and we can align the setup, analysis, and report wording where scientifically appropriate.

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Molecular Dynamics (MD)

Simulate atom-level motion to understand stability, flexibility, compactness, solvent exposure, and interaction behavior.

MD Simulation & Docking Packages

Dock Starter ($50): Fast docking screen with validation — includes 10 ligands docked against your target; Redocking validation check (crystal pose reproduced within 2 Å); Score table with ranked poses; Figures for your top 3 binding poses; Fixed price + delivery date in writing before you pay; Figures redone free until they match your format.
Validated Docking ($120): Full validation + publication-ready deliverables — includes 15 ligands docked against your target; Full redocking validation with method report; Score table, ranked poses, top-5 figures; Methods paragraph with software citations; Fixed price + delivery date in writing before you pay; Figures redone free until they match your format.
Dock-to-MD ($250): Docking + 100 ns MD simulation for your top hits — includes Everything in Validated Docking (15 ligands); Top 3 ligands simulated: 100 ns GROMACS MD each; RMSD, RMSF, SASA, H-bond, Rg plots; Short call or voice note explaining your results; Fixed price + delivery date in writing before you pay; Figures redone free until they match your format.
Dock-to-MD Complete ($399): Full study with MM-PBSA, ADMET, draft chapter + 6-month reviewer support — includes Everything in Dock-to-MD; MM-PBSA binding free energy analysis; ADMET/pharmacokinetic property screening; Full results draft chapter (ready for your thesis/manuscript); Analyses within scope requested by a reviewer — free for 6 months; Fixed price + delivery date in writing before you pay.

Single MD Run: $49 per 100 ns GROMACS simulation.

Deliverables & Outputs

Trajectory Files Full .xtc / .dcd files with topology, ready for your own further analysis.
High-Res Figures Publication-quality plots at 300 DPI — PNG, SVG, and editable .eps formats.
Methods Section Ready-to-submit methods text detailing software versions, parameters, and protocols.
Interpreted Report Scientifically written narrative contextualising results within your research question.
Raw Data Files All numerical output in .csv and .xvg format for independent verification.
Revision Support One round of peer-review revision support included with every project.

Tools & Software Used: GROMACS, CHARMM-GUI, VMD, Grace/Xmgrace, Python/R plotting

Frequently Asked Questions

Which MD analyses can you include?: Common outputs include RMSD, RMSF, SASA, radius of gyration, hydrogen bonds, distance analysis, contact maps, PCA, and free energy landscape when suitable.
Can you follow a journal-specific method?: Yes. Share the target paper or journal requirement, and we can align the setup, analysis, and report wording where scientifically appropriate.