Hi all, I am performing a Molecular Dynamics simulation of a water pore inside a membrane. I am experimenting with some analysis options and I am having a bit of a trouble understanding the water flux inside a water channel.
By looking at the literature I stumbled upon many different ways to calculate the water flux inside the channel.
For example number of molecules (inside the pore) per unit of time, or molecules passing a pre-specified area per unit of time.
First of all, which is the correct way to calculate the water flux inside a water pore in a MD simulation?
How can we be sure that by using let's say mol_num / time we aren't counting the same molecules due to hydrogen bonds? (the pore is hydrophilic, so the h-bonds are more stable and I believe that it should be taken into account)
One big thing to worry about will be the highly non-uniform velocity profile across the channel, it should be parabolic-ish as long as your are some small distance away from the walls. But if all you care about is the total flux you might not worry about this.
As far as your concern about double-counting etc. I think you should be OK if you also compute the reverse flux, and subtract the two? That way you will correct for any transient water molecule which briefly might head in the "wrong" direction.
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