1. Introduction

HydroWeb is a web-based tool for the calculation of hydrodynamic properties of macromolecules. There are three main motivations for the development of this tool:

To achieve these goals, HydroWeb offers a web interface to the following softwares:

2. Submitting calculation requests

The first step to submit a request is to choose the way the structure of the molecule will be provided. There are two possible ways, corresponding to the level of detail of the input:

Internally, these choices decide the tool that will be used in the calculations: for atomic detail level calculations HydroPro will be used, while for bead models Hydro++ will be used for rigid models, and Simuflex will handle flexible model calculations.

After indicating the detail level and the structure of the molecule, the user will have to specify some conditions for the simulation:

Finally, the user has to provide an email address to which a notification will be sent once the resuls of the calculation are available. To retrieve these results, the user will need to provide the same email address as well as the serial number assigned to the calculation, so please store this information carefully.

Once all thie information is entered, by clicking the "Submit Job" button, the information will be processed, the necessary files will be generated, and a calculation job will be issued to the worker queue in a HPC cluster.

Jobs will be processed in submission order, and the delay between the calculations submission and the results being available will be depending on the workload on the cluster, so that it is not possible to give estimations on how long the calculations are going to take.

3. Retrieving calculation results

Results are retrieved from the "Results" tab. To retrieve the result of a calculation, the user has to submit the email address that was given when submitting the calculation, as well as the Experiment ID that was issued by the system at submission time.