GROMACS version: 2019.6
GROMACS modification: No
I am trying to create a simulation box with a protein solvated in a particular solvent. I know gmx sovlate with spc216 exists, and is pretty fast. However, if I want to use another solvent like methanol, or ethanol, or hexane, etc. I don’t know if there is an easy, fast way to do this in gromacs.
At the moment, I have a methanol.pdb, methanol.itp and methanol.gro file, but when I do
gmx solvate -cp protein.gro -cs methanol.gro -o protein-solvated.gro -p topol.top
I get zero methanol molecules added to my box. If I replace methanol.gro with spc216.gro, it fills it up instantly with 10000 water molecules (box is 777 nm^3), nearly instantly.
At the moment, I am using insert-molecules -nmol 5000 -try 10000 to solvate my protein with ethanol. However, this is taking a long period of time. Is there an efficient way to perform this task, given any generic solvent?