Martini force field water bond get stretched

[demi]

GROMACS version: 2020
GROMACS modification: No

Hi community,

I am new to Gromacs, trying to understand what happened to the bonds of water molecules as shown below and how to solve it. I am simulating a polymeric gel membrane and the two slabs are fully equilibrated and then put together as shown below. But after minimization and when equilibrating this membrane, it seems some bonds were stretched unreasonable. If you could give some hints, I would appreciate it!

[giacomo.fiorin]

Hi, can this be a PBC wrapping-related visualization issue, i.e. assuming that the connectivity/topology you have loaded in VMD is correct, have you tried to use pbc unwrap or qunwrap?

Giacomo

[demi]

Hi Giacomo, I tried pbc unwrap before but the visualization is still weird. Do you have any other advice?