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This category is for discussions amongst members of the Molecular Dynamics Novice Users Interest Group that do not relate directly to GROMACS, HADDOCK or CPMD. If your question relates to one of these codes, please use the code-specific forums on this site.


i do simulation eith md web server but i cant see result and download it.can any one help me?


Hi, sure, but I would need more information!
Please open a new topic in the Molecular Dynamics Entry Level Users IG category, with information about the system you are trying to simulate, your user name in MDWeb, and the workflow you are using, and we will try to help you.
Thanks for your interest in MDWeb.


Hi, I am trying to do a structure setup after checking m y structure to prepare files for a NAMD run but when I click the same drop down menu that is in the tutorial the options do not appear. Is there a toolbox that I need to download to access those options in my dropdown menu?



Hi Lydia,

I think you are clicking the wrong button. The first button after the green check is the one you want, the “Perform a new setup operation on the selected structure”. The second one, which I think is the one you clicked, is giving you the options to “Perform a new simulation/optimization procedure”. As the structure you have uploaded is still not prepared to be used as an input for a MD simulation (see setup tutorial section of MDWeb help pages), the only simulations you can run are Coarse-Grained MDs.

See this help section as a reference for the icons meaning.

Thanks for using our server.