Use Grid Inhomogeneous Solvation Theory (GIST)

Features

• Runs protein preparation, explicit TIP3P solvation, equilibration, production MD, and cpptraj GIST in one job.
• Supports apo hydration maps centered by a reference ligand pose and holo maps that include the GAFF2-parameterized ligand.
• Returns Amber topology and coordinate files, the explicit-water trajectory, checkpoints, raw voxel tables, and OpenDX grids.
• Compares the first half of the production trajectory with the full trajectory to provide descriptive sampling-stability diagnostics.
• Uses weak positional restraints and grid RMS fitting to keep the solute and analysis region in a stable reference frame.

Statistics

Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.