GROMACS modification: No
Here post your question Thank you for helping a novice out
I am trying to insert a small molecule into a solvate bilipid layer using the command insert-molecules, but no molecules were added. I suspect it is because i need to use the -replace option. I want to know how do i specify the water molecules to replace.
Thank you so much for your help
I understood that you want to insert a molecule in place of a specific water molecules.
You can insert the molecule at specific position (specific of a water molecule) using the option of gmx insert-molecules
-ip and delete the water molecule you want to replace
you can try to have use an index file with a group with only that specific water molecule as input to gmx insert-molecules together with the option -replace
Maybe one this option works for your case
So i need to figure out which water molecules i need to replace and then specify those in the insert molecule command?