GROMACS version: 2019.3
GROMACS modification: No
I am doing umbrella sampling simulations for the two peptides in a membrane system and the reaction coordinate is the distance between the center of mass of these two peptides. I was wondering if I should use “com” or “all” for the “refcoord-scaling” option. I use Martini force field with NPT ensemble.
I have used the “all” option in the production simulations.
Thank you very much in advance for your help.
the option refcoord-scaling has effect with position restraints. See below
" Note that position restraints make the potential dependent on absolute coordinates in space. Therefore, in general the pressure (and virial) is not well defined, as the pressure is the derivative of the free-energy of the system with respect to the volume. When the reference coordinates are scaled along with the system, which can be selected with the mdp option
refcoord-scaling=all , the pressure and virial are well defined." from GROMACS Manual