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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
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Unable to open output file #22

Closed avinashkarkada closed 2 years ago

avinashkarkada commented 2 years ago

Hello.

  1. How do I visualize the output of the simulation?. I am unable to open the output xtc, pdb, dcd or trr.
  2. Is there any way to generate .tpr files?

Thank you

cpedebos commented 2 years ago

Hello,

  1. You can visualize the trajectory using VMD. You need to load both a PDB or GRO file and a trajectory file as well (XTC, DCD, TRR). For more information, refer to the VMD website: https://www.ks.uiuc.edu/Research/vmd/

  2. To generate a tpr file, you need to use the Gromacs simulation suite in your local machine. We don't use Gromacs in the notebooks.

Best, Conrado.

avinashkarkada commented 2 years ago

Hey. Would you please specify what simulation suite is used in the notebook?

Thank you

pablo-arantes commented 2 years ago

Hi,

I strongly recommend that you read the Making it Rain paper (https://pubs.acs.org/doi/10.1021/acs.jcim.1c00998), everything is well explained there. Regarding your question, in the Making it Rain code we are using OpenMM toolkit for molecular dynamics simulation (https://openmm.org/).

Pablo

avinashkarkada commented 2 years ago

Thank you!