Hi,

I am running a MD simulation using pressure coupling with absolute position restraints.

after executing the command, "gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr" GROMACS suggests me to use refcoord_scaling option.

I have searched for the refcoord_scaling and found a page (http://manual.gromacs.org/online/mdp_opt.html) where there are three option under this. They are:

refcoord-scaling:

1. no

The reference coordinates for position restraints are not modified. Note that with this option the virial and pressure will depend on the absolute positions of the reference coordinates.

2. all

The reference coordinates are scaled with the scaling matrix of the pressure coupling.

3. com

Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account.

Can any body please help me to choose the best option for running refcoord_scaling for further proceeding?

Thanks.