[gmx-users] All bulk is moving during Umbrella sampling

[gozde ergin]

Hi all,

I am doing some umbrella sampling simulation in order to estimate the PMF
profile of the system.
While doing this simulations I did:

-- Simulated the system in x*y*z box.
-- In order to have a gas phase I expanded the z coordinate to 5z and
simulate the system in x*y*5z
-- Minimization
-- Equilibration
-- Pulling
-- Than umbrella sampling.

During the umbrella sampling all of bulk molecules moved on z direction.
However the distances between the COM of pulled molecule and COM of mass
stays constant. It is not a big problem for estimating the PMF but it is a
problem when I want to calculate the pressure and density profile of the
system.

Do you have any suggestion to prevent the bulk molecules moving inside the
box?

Thanks in advance.