[gmx-users] peoblem with water
Mark.Abraham at anu.edu.au
Sat Mar 1 08:21:41 CET 2008
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.
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