How to solve :2 particles communicated to PME rank 1 are more than 2/3 times the cut-off out?

When you say that you “observed a pressure value of 0.9156 bar”, do you mean a single point observation or do you mean the average pressure over the NPT simulation (preferably discarding the first 100 or 200 ps using the -b option in gmx energy)? If it is the average, what is the uncertainty? 0.92+/-??? sounds very reasonable, especially if the system is fairly small and since the simulation time was quite short. See, e.g., Pressure is not going to 1 bar - #2 by cblau.

With a system consisting mostly of water I’d expect the density to be close to the density of the water model that you are using. I’m not sure how well, e.g., proteins and lipids in the commonly used force fields reproduce empirical densities. What is the empirical density of your polymer?