[gmx-users] peoblem with water

[Mark Abraham]

sudheer babu wrote:
> Hi all,
> I embedded protein into membrane. After that *EM and *PR running fine 
> but in position restrian intial step, one side of the membrane layer, 
> water molecules move to second side although total structure looks cubic 
> form, Only problem with diplacemnt of water to otehrside. Shall I run it 
> for  longer time? I may get equal number of water molecules both sides.

The system is periodic, so molecules will cross boundaries. You can play 
around with the options to trjconv to get the trajectory looking however 
you want to.

Mark