Fig. 2
From: Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
Example of a setup screen for MD of an protein–ligand conjugated in VisualDynamics. The VD screen shows the preparation of the molecular dynamics of the Batroxrhagin protein conjugated with the pol647 ligand. The BATROXRHAGIN.pdb, pol647.ITP, and pol647.GRO were uploaded and the parameters needed for execution were set. Next to it is a tutorial video explaining how to get the ligand files in ACPYPE. After MD analysis step, all files are available for download