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

[Dallas Warren]

Your system has a periodic boundary condition applied, so if you have a
single bilayer then all the water is part of the same water pool. So what
you observed is entirely consistent with the expected behaviour; removing
some waters leaves a void, which the remaining waters will then move to
fill.

A search of the literature is the best way to find out the methods of
introducing osmotic pressure across the bilayer, and which of the methods
might be applicable to what you are doing.

What do you mean by "uncertainties in position of some water molecules"?
Provide some screen shots (upload them somewhere on the internet for people
to access) to show what you are referring to.

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 Wed, 23 Oct 2019 at 05:29, Yogesh Sharma <yogesh.rma13 at gmail.com> wrote:

> 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.
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