I have pulled some drug molecules to the centre of a lipid bilayer using direction periodic as pull_coord_geometry for each one of them. Can I equilibrate afterwards using direction as pulling geometry and setting pull rate and pull-init as zero? Actually setting compressibility zero in z direction is not sufficient to raise the negative pressure created in water phase after pulling to 1 bar. I am using V rescale thermostat and C rescale barostat. I would also like to add that pull_coord_start = yes is being used.
Yes, but use pull-coord1-start = yes, instead of pull-coord1-init = 0.
Thank you sir