Setting up a GROMACS MD run starting from a structure file
Welcome to the GROMACS web server your entry point for molecular dynamics on the GRID. New molecular dynamics simulations are started by filling out the form below. Once submitted you will be redirected to the results page for your run where you will be informed on its progress and will be able to retrieve the results when the job is finished.
Required parameters
PDB file
Please upload a PDB file or GROMACS .gro file
Optional parameters
Simulation time
Please specify the simulation time in ns
Output resolution ns
Please specify the forcefield to use
Solvent model
Solvent model (default according to force field)
Treatment of electrostatic interactions
Please choose how to treat electrostatics
Advanced parameters
Salt concentration
Please specify the salt concentration (mol/l)
Temperature and Pressure
Specify temperature (K)
Specify pressure (Bar)
Minimal distance between periodic images
Specify minimal distance
Define specific seed
Define specific seed for random number generation (velocity distribution)
Various settings
Perform basic set of analysis on the MD results
Perform simulations in a Near-Densest Lattice Packing simulation cell
Use roto-translational constraints
Use virtual sites
Username and password
Forgot your login data?