How to properly set cell volume in GROMACS (gmx editconf)?

User discussions
1

GROMACS version:2021.1
GROMACS modification:No

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?
Many thanks

Marco

2

Dear Marco,

as far as I understand, in diglyme_cubic_box.pdb you have a single molecule, right? If yes, then first of all, you might need to build and equilibrate a box of diglyme solvent. You should probably follow what Caleman and coworkers did (Caleman et. al. 2012., Journal of Chemical Theory and Computation 8 (1): 61–74.): replicate the solvent molecule, compress it with a large pressure (~ 100 bar?), then equilibrate at your preferred temperature and pressure. You can then use the equilibrated box to solvate your molecule using “gmx solvate”.

Hope that helps.

Kind regards,

Andras Wacha

3

Hello Andras,

thank you for your answer. I tried to do the following, could you tell me if I got this right?

#1 DIG residue in topology
gmx editconf -f diglyme.pdb   -o  cubic_box.pdb -c -d 0.7 -bt cubic
gmx solvate -cp cubic_box.pdb -cs cubic_box.pdb -o solvated_box.pdb -p topol.top
gmx insert-molecules -f cubic_box.pdb -ci cubic_box.pdb -nmol 10 -o many_mol.pdb 

#substituting here 1 DIG molecule with 11 in the topology
#equilibration run ...
#nvt run ...
#npt run ...

Thank you
Marco