Closed avinashkarkada closed 2 years ago
Hello,
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/
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.
Hey. Would you please specify what simulation suite is used in the notebook?
Thank you
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
Thank you!
Hello.
Thank you