GROMACS version: 2018
GROMACS modification: Yes with plumed
Dear all,
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: #ifdef POSRES #include “posres_surface.itp” #endif
Hope this method can help you if you are looking for an alternative approach than FREEZE.