[gmx-users] Periodic boundary conditions during the simulation

[Mohamed Abdelaal]

Hello everybody,

I know that due to periodic boundary conditions the molecules move from one
side of the box to the other side and moves outside the box. I also know
how to use trjconv to solve this problem and I usually do this step at the
end of the simulation. However I have noticed that after the energy
minimization, some molecules which were position restrained at the bottom
of the box have been moved to the top of the box. I knew that I have this
periodic boundary condition problem not just from visualization of the
structure after the energy minimization, but also from the atoms
coordinates in the .gro file after the energy minimization, the z
coordinate of some atoms have been changed from bottom to top as below:

before energy minimization: (the z coordinate was always zero)

    1GRM     C1    1   0.061   0.071   0.000
    1GRM     C2    2   0.184   0.142   0.000
    1GRM     C3    3   0.184   0.284   0.000
    1GRM     C4    4   0.061   0.355   0.000
    2GRM     C1    5   0.061   0.497   0.000


after energy minimization: (z coordinate of some atoms have been changed
into 14 which is at the top of the box)

    1GRM     C1    1   0.061   0.071  14.000
    1GRM     C2    2   0.184   0.142  14.000
    1GRM     C3    3   0.184   0.284   0.000
    1GRM     C4    4   0.061   0.355   0.000
    2GRM     C1    5   0.061   0.497  14.000



Do I need to solve this PBC problem between the different steps (energy
min, NVT, NPT, production run) or it is okay to continue my simulation
(even if the molecules have moved) and solve this problem at the end ?

Many thanks,
Mohamed