The GROMACS web server online documentation
Welcome to the GROMACS web server your entry point for molecular dynamics on the GRID. GROMACS is a versitile package to perform molecular dynamics, i.e simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is able to work with many biochemical molecules like proteins, lipids and nucleic acids. The WeNMR GROMACS webportal combines the versitility of this molecular dynamics package with the calculation power of the eNMR grid. This will enable you to perform many simulations from the comfort of your internet browser anywhere in the world. The server is furthermore aimed to provide a user friendly and efficient MD experience by performing many preperation and optimization steps automatically.
Required parameters
pdb file
Upload the PDB file of the molecular system you would like to run a simulation on. The current implimentation of the server only accepts protein systems. Nucleic acids and non-peptide ligands are not supported.
Optional parameters
Simulation time
The simulation time in nano-seconds. By deafult you will be granted a maximum of 1 ns simulation time. For the time being the server is not suitable for long production runs
Output resolution
Time interval in nano-seconds in which to write a snapshot of the systems state to the trajectory file
Forcefield
Choose the forcefield to use for the simulation. GROMOS96 45a3 by default
Solvation model
Choose the solvent for the simulation. The default solvent for the choosen forcefield is used by default. These are: SPC for GROMOS; TIP3P for CHARMM and AMBER and TIP4P for OPLS
Treatment of electrostatic interactions
Select the method for treatment of the electrostatics interactions. cut-off/Reaction field is faster while Particle Mesh Ewald (PME) is more accurate
Advanced
Salt concentration
Salt concentration in mol/l. By default set to result in a isotonic environment
Temperature and Pressure
Set a specific temperature (K) and/or pressure (Bar) for the simulation
Minimal distance between periodic images
Set the minimal distance between periodic images in Amstrong. Usually set to prevent the protein from seing a periodic image of itself. This parameter is calculated automatically baed on the size of the simulation box and the size of the molecule
Define specific seed
Define specific seed for random number generation (velocity distribution)
Perform basic set of analysis on the MD results
Perform a basic set of analysis routines on the simulation results to assess the quality
Perform simulations in a Near-Densest Lattice Packing simulation cell
Calculates smallest possible simulation box for the system. This will save on CPU time. Using roto-translational constraints is advisable.
Virtual sites
Massless interaction sites constructed from atom positions
Frequently asked questions
How can I cite the GROMACS web server?
Usage of the WeNMR portals should be acknowledged in any publication:
  • The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572, www.wenmr.eu), supported by the national GRID Initiatives of Belgium, Italy, Germany, the Netherlands (via the Dutch BiG Grid project), Portugal, UK, South Africa, Taiwan and the Latin America GRID infrastructure via the Gisela project is acknowledged for the use of web portals, computing and storage facilities.