Hey everyone, I'm currently working with velocity and position data from a molecular dynamics (MD) simulation, and I could use some advice on how to analyze it. Essentially, I have data for a single particle's motion over 1000 time steps, represented as a numpy tensor with shape (1000, 1, 3). Here, 1000 is the number of time steps, 1 is the number of particles, and 3 represents the x, …

Hello all: I am doing Gromacs MD simulations of protein-ligand and it worked perfectly. However, I do not know what parameters I need to change to perform a protein-only simulation. Does anyone have some parameters for this type of simulation? Thanks all!!!! submitted by /u/Aki_kitsune9926 [link] [comments]