GROMACS version: 2018
GROMACS modification: Yes with plumed
I want to ask couple of questions in which I am facing some trouble. I want to study the wettability of droplets on different surfaces. Now coming to the questions,
How can I freeze the surface so that while the simulation is running it’s position doesn’t get changed or it doesn’t get deformed.
I have an equilibrated droplet and I want to place it above the surface suppose at a distance of say 0.6nm from the surface. I am finding this part a bit tricky. Can anybody help me with this.
Hello Dev, I have never used freeze command but I think position restraints can help you regarding this issue.
In order to do so, you can create a special index file (index.ndx) containing your atoms in the surface, say (100 atoms):
gmx_mpi make_ndx -f yourfile.gro -n index.ndx
Now you have a certain group, say number 10 in your index file: Surface (containing 100 atoms).
Once you have created the surface, we will put position restraints on them:
gmx_mpi genrestr -f yourfile.gro -n index.ndx -o posres_surface.itp -fc 1000 1000 1000
When prompted, select the particular group numver that we had created in above step, (10). This will give you a file with the name posres_surface.itp with the position restraints. Check it’s content using any text editor and refer to the manual for a better insight.
Now that, you have your position restrained file, you need to edit your .mdp files accordingly using define statement:
define = -DPOSRES
Also, edit your topology file like this:
Hope this method can help you if you are looking for an alternative approach than FREEZE.
This is what
freezegrps in the
.mdp file is for, though it is extremely artificial.
gmx editconf -center to set its position, and concatenate the coordinates with those of the surface.