Calculating the distance between fixed point and a particle and warning about absolute reference

[alevilla]

Hi,
here two posts on similar issue.

MD file error

GROMACS version: 2020.1 GROMACS modification: Yes/No Hi , there I wanted to pull a ligand out of the protein-ligand complex in the z-axis determined by fast pulling ligand method. But encountered an error during the run like this: ERROR 1 [file md.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 1 is larger than that and does not have a sp…

and

COM pulling

GROMACS version: 2018 GROMACS modification: No Dear all, I am looking for a way to restrain the center of mass (COM) of two different molecules bathed in water. The only thing close I found on gromacs that does this is the pull module embedded in the mdp files. I want to clarify that I want to restrain each molecules (COM) to a different and specific coordinate in my simulated box. Indeed the pull module has an option - pull-coord1-geometry = direction, where I can set the origin (pull-coor…

best regards
Alessandra