Re: [gmx-users] strange empty space inside the system box

Hi, Thanks a lot for the suggestion! NPT does is difficult with the frozen graphite layers. On the other hand, I have also done another simulation using the implicit graphite wall with the same polymer solution (composition and system volume). These implicit wall systems seems good, at least

[gmx-users] strange empty space inside the system box

Sounds like a bubble. Do some NpT equilibration by adding pressure coupling. That's going to be difficult with your freeze groups though. Basically, you need to find a way to get the correct solution density between the graphite layers. -- original message -- Hi all, Is there anyone who c

[gmx-users] strange empty space inside the system box

Hi all, Is there anyone who can give me some suggestions? My system is composed of some polymer chains and waters. The density of the solution is about 1g/cm^3. Then I added two explicit grahpite layers (resname=WAL) at the bottom and top of the solution, which are both freezed in three dimen