KNIME for Molecular Dynamics Simulations

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1

Hi,

I am wondering whether anyone uses KNIME for molecular simulations e.g. with GROMACS or NAMD?

Are plug-ins for GAMESS or Gaussian09?

best regards

 

2

There are not any implementations of these tools that I am aware of, but if you do want to use them in a workflow, you could always try the External Tool node.

Regards, Aaron

3

Ok, thanks.

I will give it a try.

And if anyone wants to work on it, let me know.

best Sören

4

Hi Sören,

I'm not sure if you are also interested in commercial tools - so: Schrödinger seems to have an integration for Desmond and Jaguar.

Regards,

Nils

5

Hi,

  I would like to reopen this discussion. I am really interested to use KNIME to process large datasets from MD simulations. I am using Gromacs (http://www.gromacs.org/) right now. Basically, I would like to call gromacs tools in command line. I am using Ubuntu. I guess I can call command line using javascript node or even Python node but it is not entirely satisfactory.

  I was wondering if there is/will be a Bash node available for Linux. Basically, to write Bash script and call Gromacs tools or do you think creating a node for Gromacs would be possible ?

 

   Thank you in advance.

 

      best wishes,

 

    Matthieu

6

Hi Matthieu

you could also use the external tool node.

Or, if you want to spent more time on this, generate you own set of nodes with the Generic KNIME nodes.

Cheers, Iris