GROMACS version: GROMACS modification: Yes/No Here post your question Hii, I have a dimeric protein whose RMSD plot looks a bit unusual. I am attaching the plot for reference here. I wanted to ask, that does clustering analysis for this data would help in refining the plot or would it provide some insights into the structural dyamic features of the protein? 1 …

GROMACS version: 2020.2 GROMACS modification: Yes/No Here post your question I have a protein in water, and I would like to know the pair potential energies between each water oxygen and the protein backbone for every trajectory frame to construct a spatial map of potential energy (that, eventually, I will average over time). I thought that enemat might be the way forward, but…

GROMACS version:2021.4 GROMACS modification: No Dear Gromacs Users/Developers, I am trying to include Fluoroproline (PRF) in my peptide. I got the parameters in amber FRCMOD format and have used them to modify aminoacids.rtp file. The relevant section looks like this. [ PRF ] [ atoms ] N N -0.146327 1 CD CT -0.189338 2 HD1 H1 …