GPU-accelerated infrastructure
High-performance GPU workstations run production trajectories continuously, so a 500 ns system finishes in days rather than months.
Accepting new projects
Turn your docking results into publication-ready molecular dynamics insights
GPU-accelerated MD simulations from 100 ns to 5 µs using GROMACS, Desmond and AMBER workflows — delivered with the figures, data and interpretation your manuscript actually needs.
GROMACSDesmondAMBER100 ns – 5 µsMM/PBSAPublication-ready
- 5 µs
- Longest single run
- 300–600
- dpi figure output
- 9 days
- Average turnaround
Real output from a delivered BioPC project — 25,001 frames projected onto the first two principal components.
Why researchers choose BioPC
Simulation you can defend in review
Every project is run on dedicated hardware, documented end to end, and priced before a single nanosecond is computed.
Reproducible workflows
Standardised protocols and version-controlled analysis pipelines. Every figure in your report can be regenerated from the scripts we ship with it.
Transparent pricing
A clear written quotation before any work begins. No hidden computational charges, no surprise invoices for re-runs we recommended.
Manuscript-ready outputs
Figures, statistics and supporting files prepared to journal specification, with legends you can paste directly into a thesis or submission.
- 180+
- MD projects completed
- Since 2021
- 26
- Peer-reviewed papers supported
- Q1–Q3 journals
- 5 µs
- Longest production run
- Single continuous trajectory
- 9 days
- Average turnaround
- Typical 100–200 ns project
Services
Six stages, one continuous pipeline
Commission the whole workflow or any single stage. Systems already equilibrated elsewhere are welcome — we will validate them before production.
01
System setup & equilibration
Everything between your raw structure and a stable, production-ready system.
- Protein and ligand preparation
- Protonation state assignment
- Force field selection (AMBER, CHARMM, OPLS)
- Solvation and ion addition
- Energy minimization
- NVT and NPT equilibration
- Simulation box optimization
02
Production MD simulation
Continuous GPU production runs at the timescale your question actually requires.
- 100 ns
- 200 ns
- 500 ns
- 1 µs
- 2 µs
- 5 µs (5000 ns)
- Custom simulation lengths
03
Trajectory & stability analysis
The core stability panel every reviewer expects to see.
- RMSD and RMSF
- Radius of gyration (Rg)
- SASA
- DSSP secondary structure
- Distance and angle analysis
- Convergence assessment
04
Protein–ligand interaction analysis
Which contacts hold, for how long, and what that means for affinity.
- Hydrogen bond occupancy
- Salt bridges
- Hydrophobic contacts
- Contact maps
- Interaction fractions
- Ligand torsion analysis
- Desmond Simulation Interaction Diagram
05
Advanced computational analysis
Collective motion and conformational landscapes beyond the standard panel.
- Principal component analysis (PCA)
- Free energy landscape (FEL)
- Dynamic cross-correlation matrix (DCCM)
- Covariance matrix
- Cluster analysis
- Essential dynamics
06
Binding free energy calculations
Quantitative energetics with per-residue attribution.
- MM/PBSA
- MM/GBSA
- Per-residue energy decomposition
- Energy decomposition plots
- Comparative binding analysis
Not sure which stages your project needs? Send the structure and your research question — we will scope it for you.
Get an exact quotationWhat you receive
Concrete deliverables, not a slide deck
Everything below ships with every completed project. If a journal asks for something else, we prepare it before you have to ask.
- High-resolution figures300–600 dpi raster, ready for submission
- Vector graphicsSVG, PDF and EPS for infinite rescaling
- Raw trajectory files.xtc and .trr, plus the fitted trajectories
- Topology & parameter filesFull system definition for reproduction
- Analysis scriptsEvery plot regenerable from the shipped code
- CSV / Excel data tablesThe numbers behind every curve
- Statistical summariesMeans, SD, block averages, convergence tests
- Interpretation reportA concise 2–10 page scientific write-up
- Manuscript figure legendsDrafted in journal style, ready to paste
- Supplementary packageSI figures and tables bundled separately
Sample report
See exactly what lands in your inbox
A real 500 ns protein–protein project, redacted and reformatted: the full stability panel, interaction profiling, essential dynamics and MM/PBSA decomposition, with the interpretation text we would write for your manuscript.
- · 14 publication-grade figures
- · Convergence & statistics appendix
- · Draft figure legends
- · PDF · A4 · ~2 MB
No email required.
Project workflow
From coordinates to camera-ready in five stages
You are kept in the loop at each handover — equilibration plots before production starts, and a preliminary analysis before the final report is written.
- 1
Step 1
Submit structure
PDB / ligand / project details
Send a PDB ID or your own coordinates, the ligand file, and a sentence on what you want to learn. Docking poses from AutoDock, Vina, Glide or GOLD are all valid starting points.
- 2
Step 2
System preparation
Force fields, solvation, ions
Protonation states assigned at your target pH, an appropriate force field chosen and justified, then solvation, neutralisation, minimisation and staged NVT/NPT equilibration.
- 3
Step 3
GPU production MD
100 ns to 5 µs
Continuous production on dedicated GPUs with periodic integrity checks. Replicate runs available where the question demands statistical support.
- 4
Step 4
Advanced analysis
Trajectory, PCA, MM/PBSA
The full stability panel, interaction profiling, essential dynamics and binding free energy — each plotted to publication specification.
- 5
Step 5
Publication-ready report
Figures, data, interpretation
You receive figures, vectors, raw data, scripts and a written interpretation, with a revision round included for reviewer responses.
Simulation packages
Pick the timescale your question deserves
Cost scales with system size and simulation length, so we quote per project rather than per page. These are the four configurations researchers ask for most.
100 ns
- Best for
- Thesis projects
- Typical output
- Stability analysis
- RMSD, RMSF, Rg, SASA and hydrogen bonding — the standard panel for a defensible thesis chapter.
200–500 nsMost requested
- Best for
- Journal manuscripts
- Typical output
- Convergence and interaction analysis
- Adds convergence assessment, DSSP, contact maps and interaction fractions for peer review.
1 µs
- Best for
- High-impact publications
- Typical output
- Advanced dynamics and free energy
- PCA, free energy landscape, DCCM and MM/PBSA with per-residue decomposition.
2–5 µs
- Best for
- Drug discovery research
- Typical output
- Long-timescale conformational behaviour
- Rare-event sampling, cluster analysis and comparative binding across ligand series.
Get an exact quotation
Student and multi-system rates available. Replicate runs quoted separately.
Sample results gallery
Figures from real completed projects
Every plot below came out of a delivered BioPC project and is shown at the resolution and styling you would receive. Click any figure to enlarge.
Disclaimer. These figures are shown as examples of deliverable quality only. They are not for commercial or research use. If you use any of these figures in your own research, your research will be falsified and retracted.
Research areas we support
Ten domains, one simulation discipline
The methodology transfers; the interpretation does not. Tell us the biology and we will match the protocol to the question rather than the other way round.
Drug discovery
Lead optimisation, scaffold comparison and residence-time reasoning.
Protein–ligand complexes
Pose validation and interaction persistence after docking.
Peptide therapeutics
Conformational stability and target engagement of designed peptides.
Enzyme engineering
Active-site dynamics and the effect of stabilising mutations.
Vaccine design
Multi-epitope construct stability and receptor complex behaviour.
Antibody modelling
CDR loop flexibility and antigen interface characterisation.
Membrane proteins
Lipid-bilayer embedded systems with appropriate membrane force fields.
Viral proteins
Protease, polymerase and spike-class targets with inhibitor series.
Protein–protein interactions
Interface energetics and hot-spot residue identification.
Computational biophysics
Allostery, collective motion and conformational free energy.
Track record
Work that has already survived peer review
Simulation is only useful if it holds up under a reviewer's scrutiny. These are projects where it did.
2024Journal of Biomolecular Structure and Dynamics
Multi-epitope subunit vaccine construct against a Gram-negative pathogen: immunoinformatics design and 500 ns TLR4 complex dynamics
BioPC contribution · 500 ns GROMACS production MD, DCCM, PCA/FEL and MM/PBSA
2024Scientific Reports
Identification of natural product inhibitors targeting a bacterial efflux pump: docking, ADMET and molecular dynamics
BioPC contribution · 200 ns triplicate simulations and MM/GBSA decomposition
2023Frontiers in Molecular Biosciences
Structure-based screening of phytochemicals against a viral main protease with long-timescale validation
BioPC contribution · 1 µs Desmond production run and interaction fraction analysis
2023Journal of Molecular Graphics and Modelling
Comparative dynamics of wild-type and mutant enzyme variants reveals the structural basis of thermostability
BioPC contribution · System setup, 300 ns MD and essential dynamics
The convergence assessment and per-residue decomposition answered our second reviewer almost line by line. The revision was accepted without a further round.
We sent docking poses on a Monday and had a 200 ns trajectory with the full stability panel back within two weeks — figures already at journal resolution.
What set BioPC apart was receiving the analysis scripts. We reran the whole pipeline on a second ligand ourselves without paying for it twice.
Researchers we have worked with are based at
- University of Chittagong
- University of Dhaka
- BRAC University
- Jahangirnagar University
- North South University
- Shahjalal University of Science & Technology
- Bangladesh Agricultural University
- Rajshahi University
FAQ
Frequently asked questions
The questions researchers actually send us before commissioning a project.
Which software do you use?
GROMACS, Desmond and AMBER-based workflows, selected per project. GROMACS is our default for protein–protein and membrane systems; Desmond where the Simulation Interaction Diagram is expected by the target journal; AMBER where the ligand parameterisation or MM/PBSA route calls for it.
Can you continue from my docking results?
Yes. We routinely start from AutoDock, AutoDock Vina, Glide, GOLD and HADDOCK outputs. Send the top pose (or several, if you want them compared) and we handle protonation, parameterisation and equilibration from there.
Do you provide manuscript support?
Yes. Every project includes publication-formatted figures, drafted figure legends, an interpretation report and a supplementary package. We also support one revision round for reviewer comments on the simulation work.
How long does a 500 ns simulation take?
Typically a few days to a few weeks, depending on system size and current queue load. A ~50,000-atom solvated complex generally completes within about a week of continuous GPU time; membrane systems and very large complexes take longer. You get a specific estimate in your quotation.
Do you sign NDAs?
Yes. Confidentiality agreements are available for collaborative and industry projects, and we can work under your institution's template. Unpublished structures and ligand series are never used as examples without written permission.
What do I need to send to get a quotation?
At minimum: the protein (PDB ID or file), the ligand or binding partner, and your intended simulation length or scientific question. Your manuscript deadline helps us schedule the run realistically.
How do you handle authorship and acknowledgement?
That is entirely your call. Most clients acknowledge the service; where our input is genuinely intellectual rather than technical, co-authorship can be discussed before work begins.
What if the simulation shows the complex dissociating?
We report it plainly, with the evidence. A negative result found in 200 ns is far cheaper than one found by a reviewer, and we will advise whether a different pose, protonation state or longer sampling is worth attempting.
Request a MD Service
Tell us about your system
Send what you have — even just a PDB ID and a research question is enough to start. You will receive a written quotation with a simulation plan and a realistic timeline, usually within one working day.
Direct contact
What happens next
- 1We read the systemSize, chains, ligand chemistry and the question you are asking.
- 2You get a written planForce field, timescale, analyses and a realistic delivery date.
- 3You approve, we runNothing is charged until the plan and price are agreed.