Normal mode-based geometric simulation

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Type of simulation: Small scale motions
(loops, docking ensembles, distinct starting structures)

Large scale motions
(opening and closing of domains)

Radius of gyration-guided motions
(biased simulation towards lower (or larger) ROG)

Targeted simulation

Target PDB-File  *

Rigid cluster decomposition parameters (FIRST): E-cutoff for H-bonds

Hydrophobic method

  Hydrophobic cutoff

Normal mode parameters (RCNMA): RCNMA  ENM    Cutoff for C-alpha atoms

parameters (NMSim):
No. of trajectories

No. of NMSim cycles

Side-chain distortions

Step size

  No. of sim. cycles

  Output frequency

  NM mode range          1-

  ROG mode

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 © CPC lab, 2011


Alternative sidechain conformations are not allowed.

The PDB file must not be larger than 5000 atoms.

Structural preparation before simulation:

 - Incomplete residues will be fixed.

 - Waters and ligands will be removed.

 - Hydrogens will be added (are not required for input PDB file).

You do not need to provide an email adress, a link to the results will be returned. If you provide an email address, results will also be sent to this address. Please make sure that the email address is correct. Your e-mail will not be shared with any third parties. Input files, results, and e-mails will be stored up to 7 days after which they are permanently deleted. After this point, if you need support you will have to re-submit your calculations.

SAMPLE RUN: Please, click here.

QUESTIONS? Please, have a look here.

Need help with parameters? Click here.

For questions, please do not hesitate to contact support[at]

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