GROMACS version: 2021.4
GROMACS modification: Yes/No
Here post your question : I want to simulate a system containing protein in a box of solvent (like ethanol or cyclohexane) . I am using OPLS-AA forcefield. I created the box around the protein using-
gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic
Now how do I proceed for the next step of solvation where I need to fill the box with the solvent (say cyclohexane). Can anyone kindly help me with this ?
gmx insert-molecules serves this purpose, use it with -h to see all its capabilities.
Can you please tell me the commands for the solvation steps with gmx insert? So there is no need of pre-equilibrated solvent box here?
You can use a pre-equilibrated box with gmx solvate, or just insert a desired number of molecules with gmx insert-molecules (and then equilibrate the density/pressure).
As per the help message, there’s just one obligatory input, -ci which is a structure file with your solvent molecule. You can then either set -box X Y Z to add to an empty box, or specify an existing structure with -f to add to. With -nmol you can set the max number of added solvent residues, and with -ntry you can say how many attempts to make if there’s overlap between an existing configuration and the new trial position. Many other options are probably irrelevant.
Remember to have a separate .itp with the solvent’s topology, and to add the specified number of copies to your .top file - gmx insert-molecules doesn’t do that by default.
Hi,
I would suggest you to create a topology and structure of the solvent first. Then pass the topology to the main topology as itp file, then use gmx solvate to fill the box with new molecule. you may use -cs structure_file.gro