GROMACS modification: Yes/No
I want to restrain the com of a ligand to a binding site with the flat-bottom pull code.
I want to allow for 3 Angstroms of movement away from the reference group before any force is applied to the ligand.
To accomplish this do I set my pull-coord-init value to -0.3?
Actually it must be that if the maximum distance I want between my two groups (before force is applied) is 1 Angstrom, I should set my pull-coord-init value to 0.1.
Now my issue is with the periodic boundary conditions. My simulation stops when the ligand encounters the boundary and appears separate from the binding site.
I saw that there is a pull-coord-geometry = distance - periodic but from the description it sounds like I can’t perform and NPT simulation? Only NVT?