I noticed that after gmx solvate, the molecules of interest are slightly outside the solvent box.
Might this be an issue for encountering other molecules in PBC?
How should i center the molecule in the solvent box?
My system consists of a single pdb file but with two molecule types in solvent.
before using gmx solvate, you should use gmx editconf with -c option to center your molecule
Yes i did use that option. I visualised the pdb file again and added the visuals for box itself. And tbe molecxule is inside the box. Only that it seems quite close to the edge when there is more space to better center it in the box.
Hi,
Please share your input and commands that you used
gmx editconf -f molecule.pdb -o boxed.pdb -c -d 1.2 -bt octahedron
I used this line.
GROMACS always represents the unit cell in a triclinic shape, so if you’re using an octahedron or dodecahedron, it will look weird until you re-wrap with trjconv later. Remember that there’s no such thing as “outside” in an infinite (periodic) system.
These images should help to visualise what is going on with periodic boundary condition.
