Replication Data for "Predicting the Dynamic Viscosity of High-Concentration Protein Solutions with a Chemically Specific Coarse-Grained Model"

The viscosity of high-concentration protein solutions is a critical parameter in bio-
pharmaceutical formulation development. Conventionally, the viscosity is measured
and optimized in labor-intensive experimental workflows that require a lot of material.
While predicting the viscosity with atomistic molecular dynamics (MD) simulations is
feasible, they are computationally prohibitively expensive due to the large system sizes
and the long simulation times involved. Coarse-grained MD (CG-MD) simulations sig-
nificantly reduce computational demands, but evaluating their accuracy and predictive
power requires rigorous validation. Here, we assess the capability of the Martini 3 CG
force field to predict the viscosity of high-concentration antibody solutions. We show
that a refined Martini 3 force field, with optimized protein–protein interactions, can
predict the elevated viscosities observed in concentrated solutions of F(ab’)2 fragments
of the therapeutic monoclonal antibody (mAb) omalizumab. Furthermore, we show
that our previously developed Martini 3-exc model for arginine excipients successfully
captures the trend of lowering viscosity, as observed in our rheology experiments. These
findings open the way to physics-based computational prediction of the properties of
dense biopharmaceutical solutions via large-scale MD simulations.

This dataset contains files to reproduce the data presented in the scientific letter "Predicting the Dynamic Viscosity of High-Concentration Protein Solutions with a Chemically Specific Coarse-Grained Model" by Prass et al.
The files are ordered in two directories: one with the NaCl simulations (OLIVES and GoMartini), and one with the files for the simulations with ArgCl.
In both directories, the force field files for Martini 3 and Martini 3-exc (NaCl and ArgCl, respectively) with 12% rescaling of the protein-protein interactions are given. Furthermore, each directory contains one .gro and .top file each of all repeast for the different concentrations from 150mgml to 250mgml, as well as the required .itp file of the omalizumab F(ab')2 fragments.