Solvation density issue

GROMACS version: 2021.2 / 2021.3
GROMACS modification: No

OS: Ubuntu 20.04 LTS
CPU: AMD Ryzen 9 3900X 12-Core Processor
GPU: RTX 2080 ti
CUDA: 11.4
GCC: 8.4.0

When I use gmx solvate with default options, the density is not 1000g/L.
Command: gmx solvate -cp emptybox.gro -cs spc216.gro -p -o solv.gro
I tried 4 box types as follow.
Small cubic: 1.86206 1.86206 1.86206 (same as spc216.gro file) (1000g/L)
Large cubic: 9.15513 9.15513 9.15513 (1180g/L)
Small dodecahedron: 2.00000 2.00000 1.41421 0.00000 0.00000 0.00000 0.00000 1.00000 1.00000 (1180g/L)
Large dodecahedron: 9.15513 9.15513 6.47366 0.00000 0.00000 0.00000 0.00000 4.57757 4.57757 (1180g/L)
I also used ‘-scale’ option with 0.57 and checked vdwradii.dat file has no problem.

I installed same version of gromacs on the other machine, solvent density was 1000g/L.

Because when I use same size box with spc216.gro, the density was normal, I think there is a problem on converting box step from spc216.gro to new gro file.
How can I solve this issue?

Hi young,

have you run a NPT simulation at the desired pressure and temperature to equilibrate the system (after maybe a quick energy minimization)?

I generally would never expect solvant density to exactly match the desired one after gmx solvate


I’ve run an energy minimization, a NVT simulation, and a NPT simulation.
But the problem is, my system is protein-ligand complex, and the ligand comes out from the binding pocket during the NVT simulation because there exists lots of water molecules in the pocket and they always push the ligand out. It is abnormal because if I use another machine which solvates water molecules as 1000g/L, the ligand maintains its position.

Hi Michele ,

I am curious why density after gmx solvate and npt equilibration are not matched.
Please could you elaborate on this more?

Moreover, I also want to know what are the assumptions(states of matters) during gmx solvate to fill the solute molecule.


I am not sure I understand what you mean by “assumptions”. I don’t know the inner workings of gmx solvate, I would imagine it tries to place molecules semi-randomly making sure there’s no overlap between hard spheres.

About the first part of your question, I think the answer is quite simple: after NPT equilibration the average box dimensions might change, which means that for the same number of moleucles one would get a different (average) density.

Ok . By assumptions I mean to say that weather gmx solvate considers all the atoms hard-sphere like solids or soft matters like liquids and gases.

gmx solvate has no concept of physics. It takes a pre-equilibrated solvent box and tiles it through the volume of the user-provided box. Based on van der Waals radii (tabulated in a database file), it determines if any added solvent molecules are too close to existing solute molecules or each other.