Dear gromacs users,
I am working on umbrella sampling simulations of a protein-ligand complex. I am using the protein-ligand distance as the reaction coordinate or pull-coordinate. However, I am not sure if I need to use the refcoord-scaling option in the umbrella sampling mdp file. I am currently running the simulation with pull-code options in NPT ensemble without using any options for refcoord-scaling. I am using pressure coupling options and running grompp using:
gmx grompp -f umbrella.mdp -c eq.gro -p topol.top -o prod.tpr (without any -r flag)
Is there any default option or value for refcoord-scaling? Any help would be much appreciated, thank you.