Bioinformatics Toolkit
Visualise and analyse your GROMACS trajectories directly in the browser. Upload .xvg outputs, compare simulations, and export publication-ready plots without relying on Python runtimes or external apps.
All processing happens locally in your browser; files are never uploaded to a server.
Launch GROmancer today and stay tuned as we expand the toolkit with additional molecular dynamics and bioinformatics workflows.
Upload GROMACS outputs, customise plot legends, and export high-resolution PNG charts for RMSD, RMSF, radius of gyration, SASA, hydrogen bonds, ligand torsion, interaction energies, and PCA.
Predict anticancer peptide potential using machine learning. Input peptide sequences or upload FASTA files to get predictions with 89% accuracy, feature highlighting, and 3D structure visualization.
Collaborative, audit-ready analysis environments for regulated bioinformatics pipelines with granular sharing controls.
Auto-generate publication-ready summaries that combine plots, descriptive statistics, and narrative insights for your simulation campaigns.
GROmancer: The MD Wizard is a collaborative project led by experts in molecular dynamics to make advanced analyses accessible to the community.
BioinfoXpert can extend GROmancer or tailor bespoke dashboards for your simulation pipelines. Reach out and let’s build the tooling you need.
Contact BioinfoXpertProcess GROMACS simulations entirely in your browser. Upload one or more .xvg files per tab, tweak legends, and export plots at 300, 600, or 1200 dpi.
Select an analysis type, upload your files, customise legends, and download publication-ready PNGs in seconds.
Compare structural deviation across one or more trajectories. Upload matching .xvg files and adjust legend labels to match your systems.
.xvg filesProtein or protein-protein complexes:
gmx rms -s your_protein.tpr -f your_protein.xtc -o rmsd.xvg -tu nsWhen prompted, choose group 4 ("Backbone") for both fitting and RMSD calculation. The -tu ns flag converts picoseconds to nanoseconds.
Protein-ligand systems:
gmx rms -s your_protein.tpr -f your_protein.xtc -n index.ndx -tu ns -o rmsd_ligand.xvgSelect group 4 ("Backbone") for alignment and your ligand group for RMSD. Detailed walkthrough: MD Tutorials for GROMACS.
Visualise per-residue flexibility and compare residue-level motion across systems.
.xvg filesUse for protein, protein-protein, or protein-ligand trajectories:
gmx rmsf -s your_protein.tpr -f your_protein.xtc -o rmsf.xvg -resSelect group 3 ("C-alpha") when prompted. Tutorial reference: MD Tutorials for GROMACS.
Monitor the compactness of your system over time to assess structural stability.
.xvg filesApplicable to protein, protein-protein, and protein-ligand systems:
gmx gyrate -s your_protein.tpr -f your_protein.xtc -o gyrate.xvg -tu nsChoose group 1 ("Protein"). The -tu ns flag outputs time in nanoseconds.
Track changes to solvent exposure across your simulation timeline.
.xvg filesCommand for protein, protein-protein, or protein-ligand trajectories:
gmx sasa -s your_protein.tpr -f your_protein.xtc -o sasa.xvg -tu nsSelect group 1 ("Protein"). Use -surface or -output flags if you need per-residue details.
Quantify hydrogen bond formation across time for intra- or inter-molecular interactions.
.xvg filesRun for protein, protein-protein, or protein-ligand systems:
gmx hbond -s your_protein.tpr -f your_protein.xtc -num hbond.xvg -tu nsSelect the donor or acceptor groups of interest when prompted. The -tu ns flag converts picoseconds to nanoseconds.
Inspect ligand dihedral angles across the simulation to check conformational stability.
.xvg filesFor protein-ligand trajectories:
gmx angle -f traj.xtc -n angle.ndx -type dihedral -o dihedral.xvg -ov dihedral_avg.xvgSelect the atoms defining the dihedral from your index file. The average output (dihedral_avg.xvg) is optional.
Plot Coulombic (Coul-SR) and Lennard-Jones (LJ-SR) interaction energies over time for ligand-receptor systems.
.xvg filesUse gmx energy and select Coul-SR and LJ-SR terms:
gmx energy -f ener.edr -o interaction_energy.xvgWhen prompted, choose the Coul-SR and LJ-SR energy components. The plot shows both traces for each uploaded file.
Upload PCA projections (.xvg with eigenvectors) to generate scatter plots with extracted axis labels.
.xvg filesAfter running gmx covar and gmx anaeig, export the projection:
gmx anaeig -v eigenvec.trr -f filtered.xtc -first 1 -last 2 -proj pca.xvgThe plot automatically reads title and axis labels from the file headers.