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

[Dallas Warren]

Elementary chemistry calculation:

# molecules = Na*C*V
Na = Avagadros number
C = concentration
V = volume

Use that to set the correct number of waters in a given partial box of
correct shape and volume to give the target concentration.

If you are after something beyond that, and I've misinterpreted what you
are asking, you need to be following the protocol/procedure from the papers
you are using to perform this simulation/calculation.

However, it seems to me that you still have the issue with how you are
creating the pressure differential. From what you have said you don't have
a way to deal with that. Run NTP, box will contract. Even if you run NTV,
membrane(s) will move in the z direction to equalise pressure. Hopefully
you have something sorted out there, if not, search the literature and
follow the procedure for doing these types of simulations.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 24 Oct 2019 at 20:54, Yogesh Sharma <yogesh.rma13 at gmail.com> wrote:

> Thank you Dr. Dallas
> But my concern is setting water concentration difference in exterior and
> interior of cell membrane not box size adjustment. Is there any way or some
> scripts available to do so?
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