GROMACS version: 2023.2
GROMACS modification: No
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I have done a MD simulation in GROMACS for my protein-lipid bilayer system generated using CHARMM-GUI. Protein is a bacterial fluc channel (5a43), and lipids are DPPC.
During equilibration and also in the production runs, I used V-rescale and C-rescale as the thermostat and barostat respectively. The simulation temperature was 323.15K. Other parameters are usual parameters used in membrane simulations.
I want to confirm whether the RMSD is converged and also I hope for advice from experienced people in present-day MD simulations, about the novel C-rescale barostat. I have seen people are using PR for the production runs often. Is there an advantage of using PR over C-rescale in the production runs? However, I got “pressure scaling is more than 1%” warnings when I was using PR in my previous attempts at this simulation even after the system is equilibrated in m)ultiple steps (as given by CHARMM-GUI mdp files) and longer time scales (1+!+1+5+10+30* ns - * without any constraints). I did not get any warinings when I use C-rescale.
Here is the RMSD curve,
Here is the final structure achieved by the simulation.
System size,
