GROMACS version: 2021.4
GROMACS modification: Yes/No
Here post your question : I wanted to simulate a biphasic system, so I am following the tutorial of water-cyclohexane system, but I have a confusion here that after placing the protein in water-cyclohexane biphasic system, do I need to proceed from solvation step, then adding ions, etc. as in the lysozyme tutorial? Is the solvation step needed here? From which step should i proceed ?
Hi,
If I understand it correctly, you are at the final step of the tutorial, having a simulation box with the peptide in the upper half and cyclohexane in the lower half, am I right?
You can solvate with water by using gmx solvate and giving your current system as -cp. Basically your “protein” now is the peptide+cyclohexane system, without water.
Thank you for helping.