A worldwide e-Infrastructure for NMR and structural biology

Getting started with GROMACS

Like AMBER, GROMACS s a suite of programs for molecular simulations. GROMACS is freely available, open source and known for itsversatility and performance. Unlike most other packages, GROMACS is not linked to a specific force field, but can perform simulations with any force field that has been ported to the file format required. Available force fields include recent versions from GROMOS, AMBER, CHARMM and OPLS.

 

 

How to use the GROMACS web server?

The GROMACS web server provides two web interfaces to setup a molecular dynamics run:

  • Starting a MD run from a PDB file: This is the default interface were the molecular dynamics run is started from only a PDB file as required input. Optionally the simulation time (default 1 ns), output resolution and forcefield (GROMOS96 53a6 by default) can be chosen. By default the used solvent model and treatment of electrostatics will be set to those used during parameterization of the forcefield although they may be set differently. Finally a set of advanced parameters may be set although they all default to best practice values. These include; temperature, pressure, salinity and minimal distance between periodic images. Other options supported in the advanced settings are use of "virtual sites", the use of a Near-Densest Lattice Packing simulation cell, the use of roto-translational constraints and a final set of quality analysis routines (on by default). Using these settings the server will prepaire the simulation system using a protocolized workflow described below.
  • Starting a MD run from a GROMACS binary run input file: Next to starting a molecular dynamics run from a PDB file, the GROMACS web server supports upload of pre-made simulations systems using the GROMACS binary run input file format (.tpr files) and optional checkpoint files (.cpt). A binary run input file contains all information needed for the main GROMACS MD engine (mdrun exacutable) to perform the simulation and it is the same file created by the protocolized workflow used by the PDB interface. This interface thus allows to perform simulations on systems with topologies, forcefields and/or custom setup procedures not supported by the PDB interface. 

Both interfaces will create a GROMACS web server project for which its progress can be followed from its own project page. The GROMACS web server is designed to perform long MD simulations in parts. The project page provides an overview on the progress of every simulation part and the simulation as a whole. The user can interact with the running simulation by analyzing all simulation parts performed upto that moment, resubmission of the last simulation part in case of grid related failures, extending the simulation or aborting it altogether. Major changes in the status of the project will also be communicated via email.

 

How does the GROMACS web server perform protocolized simulations?

The GROMACS portal now made operational within WeNMR interfaces to a protocolized, yet flexible GROMACS workflow. The workflow starts with generating a topology for protein and nucleic acid chains, according to the force field specified. The resulting structure is energy minimized and subsequently solvated in a periodic unit cell. By default, a rhombic dodecahedron unit cell is used for solvation, being the most optimal regular unit cell available, with a distance between periodic images of 2.25 nm. The solvent added is a sodium chloride solution with excess charge compensating the net charge of the solute, and a total concentration that defaults to isotonic (0.1536 M), but can also be set explicitly. Following solvation, the system is energy minimized again, after which a series of molecular dynamics simulations is run to equilibrate the solvent, the temperature, and the pressure, respectively. The systems are weakly coupled to a heat bath of 300K and an ambient pressure of 1 bar, unless specified otherwise. The coupling is effected by the V-rescale thermostat and the Berendsen manostat, respectively. The type of solvent and the treatment of long range electrostatic interactions used depend on the force field, corresponding to the conditions under which the force field was parameterized. However, these default settings can be overruled by the user. After equilibration, a short run is performed under production simulation conditions, followed by the production simulation itself. Through the WeNMR GROMACS portal, production simulations are restricted to 1 ns simulations for users with default permission settings, which should be sufficient to assess stability, e.g. of NMR derived structures. Permissions may be upgraded to allow for 10 ns or 50 ns simulation times upon request. Although such time scales do not allow full functional characterization, they have been shown to suffice for assessment of the effects of differences between simulations. On top of this, the portal may serve an important role by providing the users with equilibrated, production ready simulation systems.

 

How do I get access to the GROMACS web server?

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.
  • 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.
  • Once you are a member of the WeNMR VRC it is easy to subscribe to the many services WeNMR has to offer.

 

Links

 

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life