Minimal example of refcoord_scaling barostat artifact

Coarse-grained MD simulation of the SARS-CoV-2 E protein (PDB ID: 5X29) embedded in 100% POPC lipids (12nm X 12nm). Unless otherwise noted, all simulations were performed using GROMACS 2016 and the Martini 2.2 force field. The Berendsen thermostat was set to 313 K and a semi-isotropic Berendsen barostat was set to 1 bar in both directions. The compressibility modulus in both dimensions was 3 × 10−5 bar−1 with time constant 3 ps. Electrostatics and van der Waals (vdW) were shifted with a cutoff r-value of 1.2 nm. All systems underwent 100,000 steps of steepest-descent energy minimization prior to MD simulation with a timestep of 0.025 ps. Protein back-bone beads were restrained to their initial coordinates via harmonic potential with a force constant of 2,000 kJ mol−1 nm−1. We describe this style of restraint as “absolute position restraints". The refcoord_scaling parameter was set to "all."