Potential error when I merge 3 cells

User discussions
1

Dear all,

I am doing a simulation to investigate water transport through a membrane. As depicted in the photo, the middle zone is a pre-relaxed polymer/water system. Briefly, first, I increased the length of mentioned system in the x-direction then I added two water reservoirs on each side. note that all the systems are in a large box. But, when I try to do relaxation in NVT level I face with this error:

Fatal error:Step 0: The total potential energy is 4.72896e+15, which is extremely high. The LJ and electrostatic contributions to the energy are 4.72896e+15 and -103846, respectively. A very high potential energy can be caused by overlapping interactions in bonded interactions or very large coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology.

Also, some errors are shown when I do minimization.

What is the main problem? Why increase in the box size lead to this error?

Thanks alot

box
box1086×588 204 KB

2

For friends who have a similar problem:

I added :
pbc-molecules = yes
to .mdp file and the problem is fixed.

4

You may want to refer the “pbc” keyword, there is not a “pbc-molecules” keyword to use in mdp file.