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

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Mon Jan 25 01:20:30 CET 2010

I suggest you first can run a system with only polymer solution in NPT
ensemble. After a suitable density is reached, then you can add two
graphite sheets into the equilibrated system, please set the distance
between graphite and solution carefully (or trial error).

Best wishes,


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 the empty space is not there. Any other idea about it?

best regards,
Baofu Qiao

chris.neale at utoronto.ca wrote:
> 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,

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