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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
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Molecular Simulation on Protein Ligand Complex in Gromacs #23

Closed atultiwari closed 2 years ago

atultiwari commented 2 years ago

Hi,

First of all, thank you very much for this awesome work. However, I am only familiar with Gromacs. I see that there is one Gromacs_input file but that uses protein only. I wanted to know how to perform molecular simulation on protein-ligand complex in gromacs by this method.

Thank you

pablo-arantes commented 2 years ago

Hi @atultiwari,

Sorry for my late reply. Regarding your question, If you check the Making it Rain paper (https://pubs.acs.org/doi/10.1021/acs.jcim.1c00998), everything is well explained there. We are not using Gromacs for MD simulations. In the Making it Rain code we are using OpenMM toolkit for molecular dynamics simulation (https://openmm.org/). OpenMM toolkit is able to read the Gromacs format files and proceed with the simulations. If you want to run MD simulations of protein-ligand complex, you can use our protein-ligand notebook or our notebook that recognize Gromacs files (https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Gromacs_inputs.ipynb).

Thank you.

Best,

Pablo

atultiwari commented 2 years ago

Hi,

Thank you for your reply. Unfortunately my institute does not provide access to the journal in which the article is published, and I cant afford to purchase the access to article at an individual level. So, I couldn't read it. But my query is well answered in your reply.

Thank you

pablo-arantes commented 2 years ago

Hi @atultiwari,

Sorry for that. You can check the preprint (https://chemrxiv.org/engage/chemrxiv/article-details/6116a01f424ea3ed758921a7), is almost the same paper. I'm closing the issue now.

Thank you.

Best,

Pablo