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 topol.top -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?