Hello, I would like to solvate a molecule (TFSI+) into a solvent (diglyme).
Both pdb files were downloaded from LigParGen.
I try to modify the geometry with gmx editconf as follows, then gmx solvate:
gmx editconf -f TFSI.pdb -o TFSI_cubic_box.pdb -c -d 1.0 -bt dodecahedron ## new box volume : 14.46 (nm^3) gmx editconf -f diglyme.pdb -o diglyme_cubic_box.pdb -c -d 0.7 -bt cubic. ## new box volume : 16.12 (nm^3) gmx solvate -cp TFSI_cubic_box.pdb -cs diglyme_cubic_box.pdb -o cubic_box.gro -p topol.top
and get a final box with very low density (47 g/l) and 1 solvent molecule:
Output configuration contains 38 atoms in 2 residues Volume : 14.4631 (nm^3) Density : 47.6845 (g/l) Number of solvent molecules: 1
According to other tutorials online, I would expect a much higher density, around 1000 g/l and a larger number of solvent molecules ~1000.
I tried to run editconf with “-density 200” on top of diglyme_cubic_box.pdb before solvate and it kind of works: I get an higher density but all solvent molecules are perfectly overlapped.
How can I get something meaningful in this context?