# Solvatation of coarse-grained system with gromacs **URL:** \ **Category:** User discussions\ **Created:** [March 21, 2025, 2:55pm UTC](https://gromacs.bioexcel.eu/t/solvatation-of-coarse-grained-system-with-gromacs/11785 "2025-03-21T14:55:02Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![danieljean](https://avatars.discourse-cdn.com/v4/letter/d/a698b9/32.png) [@danieljean](https://gromacs.bioexcel.eu/u/danieljean)\ **Post date:** [March 21, 2025, 2:55pm UTC](https://gromacs.bioexcel.eu/t/solvatation-of-coarse-grained-system-with-gromacs/11785/1 "2025-03-21T14:55:02Z")
I solvate the protein system described in the martini tutorial ([martini-workshop/02\_protein\_basics/tutorial.md at main · marrink-lab/martini-workshop · GitHub](https://github.com/marrink-lab/martini-workshop/blob/main/02_protein_basics/tutorial.md)) and I get the following result: Output configuration contains 11142 atoms in 10637 residues Volume : 1300.18 (nm^3) Density : 2433.53 (g/l) Number of solvent molecules: 10254 Obviously, the density is out of range. But if you perform a simple calculation to get the density from the box volume and the number of water beads the result is: with 72g as the mass of a water bead (4 normal individual water molecules). Mass of water used for solvatation: 10254 X 72 /6.022 X 10^-23 = 1.226 X 10^-18 g Volume of the box: 1300 X 10^-24 = 1.3 X 10^-21 L Density: (1.226 X 10^-18) / (1.3 X 10^-21)= 943 g/L, which is a reasonable value not very far from 1000 g/L considering that the protein mass is not taken into account. It appears that there is a bug in the calculation of density. Is it important for the following operations of simulation ? In all the cases I’ve tried, the NPT equilibration is not very good with a big RMSD (usually more than 50 bar for a target pressure of 1 bar). So what’s wrong? Thanks for your comments