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:

  • Simulation (Single Structure): Work from a structure, setup and run an MD simulation, run a coarse-grained MD.
  • Analysis (MD Trajectory): Work from a trajectory, analyse, get information or convert between MD trajectory formats.
  • DNA/RNA Simulation from Sequence: Work from a sequence, obtain a 3D structure from a nucleic acid sequence.
  • Upload past MDWeb Project: Upload a stored MDWeb project.
New Project

If Simulation (Single 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 Analysis (MD 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 past MDWeb Project option allows MDWeb users to upload projects, previously strored using the Download Project utility.

Upload Project

Upload Project

The DNA/RNA Simulation from Sequence option allows MDWeb users to upload a nucleic acid sequence, directly or from FASTA file, in order to obtain a 3D structure. User have different kind of final structures to choose:
  • Right Handed B-DNA
  • Left Handed B-DNA
  • Right Handed A-DNA
  • Right Handed A-RNA
  • Right Handed A'-RNA
  • User Defined DNA/RNA: Possibility to change a set of helical parameters.
  • DNA generated using ABC average helical parameter values. Sequence-dependent: each base pair step is assembled using corresponding average helical parameters.
  • DNA generated using experimental X-ray average helical parameter values. Sequence-dependent: each base pair step is assembled using corresponding average helical parameters.

Input From Sequence

Input from Sequence