MDWeb interface

MDWeb interfaceMDWeb holds a personal workspace where structures and trajectories are stored.

Data is structured in "projects". A project is opened with an initial structure or trajectory. All operations are based on that initial input.

Data in the project is organized in a tree that outlines the history of every object back to the initial one.

Structures and trajectories are added to the tree once available.

The available operations and workflows are defined according to every data type.

User Registration

User IdentificationMDWeb gives the possibility to work as an anonymous user, or as a registered user.

Warning: Anonymous users' projects will be removed once disconnected or when session expires (after some minutes of inactivity).

On the other hand, Registered users' projects will be stored in our disks for a reasonable time. A capacity of 2 GB of disk space will be assigned for each registered user.

New Project

MDWeb offers three main entry options:

  • Base Structure: Work from a structure, setup and run an MD simulation, run a coarse-grained MD.
  • Base Trajectory: Work from a trajectory, analyse, get information or convert between MD trajectory formats.
  • Upload Project: Upload a stored MDWeb project.
New Project

If Base Structure option is chosen, user will be redirected to the Structure Checking page.

(*) Please note that user provided structures must follow PDB File Format v.3.30 (July 13, 2011). The most relevant points to consider are:
  • A Non-blank alphanumerical character is used for chain identifier.
  • Non-polymer or other “non-standard” chemical coordinates, such as water molecules or atoms presented in HET groups, use the HETATM record type.
If Base Trajectory option is chosen, a new project is created with the input trajectory as a tree root (base object to work with). (See Workspace)

Note that MDWeb has a limit file size of 100 MB.

Different input files are required depending on program and trajectory formats (NAMD/Amber/Gromacs). Gzipped files are accepted.

Gromacs Trajectory Input Files

Gromacs Trajectory Input Files Example

NAMD/AMBER Trajectory Input Files

NAMD/Amber Trajectory Input Files Example

The Upload Project option allows MDWeb users to upload projects, previously strored using the Download Project utility.

Upload Project

Upload Project