- The GROMACS web server
Welcome to the GROMACS web server your entry point for molecular dynamics on the GRID. GROMACS is a versatile 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 web portal
combines the versatility 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 preparation and optimization steps automatically.
- The use of the GROMACS web server is free of charge for academic users, scroll down for more information
- For more information about GROMACS, visit their website
- More information about the GROMACS web server is available in the online documentation
- Questions, suggestions, problems? Contact us via the GROMACS WeNMR Help Center
- Presenting the all new GROMACS web portal offering longer maximum simulation times, improved stability,
advanced interactive controls and the ability to start a simulation from a GROMACS binary run input file.
- The GROMACS server interfaces
- Important Notes
- The GROMACS web portal applies a fare share policy to resources by constraining simulation parameters based on user
- By default you will be granted "easy" access privileges which allow you to run 10.0 nanoseconds
simulations on molecules restricted to 1200 residues. You are restricted to
5 active projects at any time
- You may apply for additional privileges by email. These are "expert" with a maximum of 20.0
nanoseconds simulation time and 10 active projects or "guru" privileges with
50.0 nanoseconds maximum simulation time and 20
- Your simulation results will be stored on the server for a maximum of 7 days after completion
- When starting a simulation from a PDB or GROMACS coordinate file please note that nucleic acids systems are not
fully supported yet, you might encounter problems. None-standard residues including membrane systems and ligands
are not supported in this interface either
- You can use the second server interface to upload ready made GROMACS binary run input files (.tpr) and optional checkpoint
files (.cpt). These files do allow you to perform simulations on systems that require a different protocol for system setup
or contain residues not supported by the default topology database of the GROMACS distribution on the Grid.
- Server Statistics
||Number of users:
|Number of active jobs:
|Number of served jobs:
|Number of queued jobs:
- How to Signup for an Account?
- The GROMACS web server is free of charge for academic users. Access to the server is managed through Single Sign On authentication using
your WeNMR account. Old style GROMACS web server accounts are still supported. How to proceed:
- Become a member of the WeNMR Virtual Research Community at www.wenmr.eu
- Once logged in, go to the "My Services" tab in you account profile and subscribe to the GROMACS web portal. Follow the instructions
on screen. GROMACS requires a valid X509 Grid certificate as explained below
- You have to be in possession of a valid X509 personal certificate that proves that you are allowed to run calculations on
the GRID and a membership of the eNMR Virtual Organization If you do not yet have one you can find information about obtaining a certificate
- Once you are a member of the WeNMR VRC it is easy to subscribe to the many services WeNMR has to offer
- Forgot your login credentials? For old style GROMACS web portal accounts you can request a copy of your login data using
your email address here. For Single Sign On accounts use the "Forgotten password" option
of the WeNMR web site.
- Bug reporting and version history
- Although the server has been tested extensively there is always a possibility that you run into a bug.
In case this happens the server will either report the error on the results page of your run or it will be reported in on
of the log files in the tar zipped archive you can download. Please report the error any other question to us by
- For GROMACS specific questions please refer to the GROMACS website for answers
||Proud to present an all new version 2 of the GROMACS web portal. We now support longer simulation times starting with a default
of 10.0 nanoseconds. Advanced project controls allow you to interact with the
running project and perform such tasks as analyzing the trajectories at any time, extending the simulation time of a finished
project and resubmitting failed simulation parts to ensure continuation of the simulation.
A second server interface allows you to upload pre-made GROMACS binary run input files (.tpr files) and optional checkpoint files
(.cpt files) to simulate systems you have prepared yourself or continue previously run simulations.
||The GROMACS server is multi-threading enabled using 6 cores by default. Please notify use in case of errors
related to domain decomposition
||Initial release of version 1.0 of the GROMACS web portal
- Citing WeNMR GROMACS web portal
- Usage of the WeNMR portals should be acknowledged in any publication:
- M. van Dijk, T.A. Wassenaar and A.M.J.J. Bonvin (2012).
A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.
J. Chem. Theory Comput. 8, 3463-3472.
- T.A. Wassenaar, M. van Dijk, N. Loureiro-Ferreira, G. van der Schot, S.J. de Vries, C. Schmitz, J. van der Zwan, R. Boelens, A. Giachetti, L. Ferella, A. Rosato, I. Bertini, T. Herrmann, H.R.A. Jonker, A. Bagaria, V. Jaravine, P. Guntert, H. Schwalbe, W.F. Vranken, J.F. Doreleijers, G. Vriend, G.W. Vuister, D. Franke, A. Kikhney, D.I. Svergun, R. Fogh, J. Ionides, E.D. Laue, C. Spronk, S. Jurka, M. Verlato, S. Badoer, S. Dal Pra, M. Mazzucato, E. Frizziero and A.M.J.J. Bonvin (2012).
"WeNMR: Structural Biology on the Grid."
J. Grid. Comp., 10, 743-767.