MDWeb is a web interface to perform molecular dynamics simulations or analyze molecular dynamics trajectories.
Since first simulation of biomacromolecules in 1977, molecular dynamics (MD) has experienced a long evolution, and, at present, it is a mature technique that can be used to obtain an accurate picture of the dynamics of complex systems with atomistic detail.
Despite all its power the practical use of MD is limited by three factors:
i) the uncertainties of classical force-fields.
ii) the required computational power.
iii) the high level of expertise needed to use the technique.
Focusing in the last point, it should be remarked that setting up a system for simulation requires from the combination of a series of operations, many of them to be performed manually, and a number of decisions that demand a significant degree of expertise. The end result is that newcomers to the field face a stiff learning curve and that in some cases (for example when supercomputer resources are used) setting-up of simulations can represent a period of time similar to that of deriving the trajectory. These problems reach a maximum in high-throughput projects, where thousands of trajectories need to be launched, what forces the development of automatic tools for mimicking human expertise in launching (and then analyzing) MD trajectories.
Within the MoDEL project we have developed a series of tools that allowed us to launch and analyze around 2,000 trajectories with little human intervention. An evolution of our original workflows is made available here as a general tool, not linked to any specific simulation package, to help naïve users to prepare completely systems for simulations, and that allows expert users the use of MD in the high-throughput regime.
The software tool developed here is presented as a fully integrated web-services-oriented software platform to perform molecular dynamics (MDMoby), and its web portal MDWeb. The technology has been adapted to be accessed as web-services following the BioMoby framework. MDMoby can be accessed with web-services clients and also programatically through suitable APIs (INB-BSC). A number of pre-prepared pipelines are also available to help non-expert users in the use of standard simulation procedures.
The web portal MDWeb provides a friendly environment to setup new systems, run test simulations and perform analysis within a guided interface. Setup files can be prepared for Amber, NAMD, and Gromacs (other formats will be incorporated in the future) and analysis can be carried out using any standard trajectory format.
Additionally, the platform is interfaced to our flexibility analysis software FlexServ, so providing coarse-grained simulation, and advanced flexibility analysis tools.
Manual / Tutorial
MDWeb is extensively documented in this on-line help. Information about operations and workflows, explanations about how to use the server, tutorials for each of t
he main parts of it, all of that can be found in these pages.
The majority of this information can be also found in MDWeb Manual and Tutorial [PDF]: