[gmx-users] setting up osmotic gradient across bilayer.

[Yogesh Sharma]

Hello users

I am trying to check water transport through a membrane protein. I ran
simulation for 10 ns. In first attempt I couldn't see significant transport
through protein although pore was filled. I hypothesized it could be due to
osmotic equilibrium. so in my next mdrun I deleted all water molecules
between z coordinate 0 to 1.2 A. Unexpectedly whole set up shifted down to
fill up empty spaces left by water molecule deletion. Although I got some
water molecules transporting through bilayer but in opposite direction. now
i am confused if its artifact or protein is solely exporter.
 My query is how can i set up a osmotic potential across bilayer
effectively?
During visual trajectory analysis by vmd, in sequential frame I observed
uncertainities in position of some  water molecules (even across bilayer) .
Does it mean my system has crashed?


your guidance will be highly appreciated.
thank you in advance.