[gmx-users] refcoord_scaling

Hi, I have a question about refcoord_scaling option and its role in pressure coupling. What I'm currently doing is just running the lysozyme tutorial on my own protein. I've so far had successful runs when equilibrating on my own machine, which is currently running gmx4.5.3. NPT came to a stable av

[gmx-users] g_rms on large amount of data

Hi, I'm using Gromacs 4.5.5 to simulate a protein in explicit solvent. The simulation is running fine and I have collected 9 100ns simulations. I'm eliminating the first 50 ns for equilibration and sheer data size. What I want to do now is to cluster the simulations based on rmsd of certain residue