Browse Code
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure stable performance during parallel processing. Beyond simulation execution, it includes advanced trajectory processing and analysis tools such as RMSD, RMSF, SASA, clustering, PCA, hydrogen-bond analysis, Ramachandran plots, and FEL mapping. With integrated visualization and plotting utilities, it offers a unified platform for researchers, educators, and students to perform complete MD workflows efficiently and reproducibly. Our Goal is to bring MD simulations to every biologist's toolkit.
Features
- A complete and unified simulation platform supporting parallel execution of Gromacs commands while monitoring system resources such as CPU, RAM, and disk usage in real time to maintain system stability.
- The software organizes the entire MD workflow into structured tabs maintaining the traditional Gromacs workflow, covering system preparation, solvation, ion addition, minimization, equilibration, production runs.
- Utility for managing the periodic boundary conditions and perform trajectory preprocessing (pbc nojump, pbc whole, fit, rot, trans etc)
- User friendly trajectory data management like, trajectory concatenation. Separation of frames from the trajectory and subsequently save in various file formats like pdb and xtc.
- Molecular Stability (RMSD, RMSF, RG, SASA) calculation, visualization and analysis
- Stereochemical monitoring in simulations (2D and 3D ramachandran Plots)
- Hydrogen bonding calculation, visualization and analysis (number, strength, lifetime, running average, distribution and much more)
- Noise reduction and dimensionality reduction in the multidimensional MD data. PCA calculation, visualization and analysis
- Free Energy Land Scape calculation, visualization (Support data from Gromacs and NAMD)
- Conduct cluster analysis effectively (set-up the clustering job, customizable RMSD Cutoffs, index specific cluster analysis etc. Support trajectories from Gromacs and NAMD)
- An independent functionality for collective plotting and visualization of general analysis tasks like RMSD, RMSF, RG, SASA.
- Plotting the data from PCA, like PCA Eigen values and PCA projections
- Plotting the data from Ramachandran Plot for in-depth details of the stereo-chemical behaviour of the biomolecular system in the trajectory like angle density and phi and psi distribution
Project Samples
