Input Structures

Structures to perform the GOdMD calculation could be obtained from PDB (include chain code if necessary) or provided as PDB formatted files.
CA atoms of the target structure will be used as reference for the simulation. The remaining atoms will be discarded. Residue identity is not required, but both structures should contain the same number of residues and ordering should match the appropriate sequence alignment.
Structure to be simulated (Mandatory): Target structure (Mandatory):
PDB Code Id (ex. 1ake_A) PDB Code Id (ex. 4ake_A)
User provided (PDB format) User provided (PDB format)


Temperature (K) Relaxation Window: Short Medium Long
Desired final RMSd (Å): Automatic User-defined:
Short Relaxation Window ~ 20ps of stationary dynamics; Medium ~ 50ps; Long ~ 100ps.
Simulation will stop when the desired RMSd is obtained or manually at any time.
Non-converging simulations will be stopped automatically after an equivalent time of 200 ns of simulation time.

E-Mail address (Mandatory):

You will be notified by email when results are available.
Please, make sure that the message is not blocked by your anti-spam filter.
Results will be available for download during 30 days.