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KNIME for Molecular Dynamics Simulations

Member for

5 years 7 months serendip42

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

 

Comments
Thu, 01/30/2014 - 11:59

Member for

7 years 3 months

Aaron Hart

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

Fri, 01/31/2014 - 12:32

Member for

5 years 7 months

serendip42

Ok, thanks.

I will give it a try.

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

best Sören

Sat, 03/01/2014 - 10:02

Member for

9 years 4 months

weskamp

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

Wed, 06/08/2016 - 05:03

Member for

3 years 3 months

matth_C

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

Thu, 06/09/2016 - 01:34

Member for

9 years 3 months

Iris

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